Genetic Variant ENST00000284414.4:n.923C>T (chr10-27249640-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000284414.4(ENSG00000293149):n.923C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,324,402 control chromosomes in the GnomAD database, including 29,304 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 2810 hom., cov: 32)

Exomes 𝑓: 0.20 ( 26494 hom. )

Consequence

ENSG00000293149
ENST00000284414.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

4 publications found

Variant links:

COSMIC-nc: COSV52632178

Genes affected

ENSG00000293149 (HGNC:):

ENSG00000293149 links:

LRRC37A6P (HGNC:33746): (leucine rich repeat containing 37 member A6, pseudogene)

LRRC37A6P links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000284414.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000284414.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC37A6P	NR_003525.2		n.2667C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000293149	ENST00000284414.4	TSL:6	n.923C>T	non_coding_transcript_exon	Exon 1 of 1
LRRC37A6P	ENST00000448648.2	TSL:6	n.2154C>T	non_coding_transcript_exon	Exon 1 of 1
ENSG00000262412	ENST00000574842.2	TSL:2	n.298-418G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28326

AN:

152000

Hom.:

2803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.0135

Gnomad SAS

AF:

0.0534

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.170

GnomAD2 exomes

AF:

0.177

AC:

44476

AN:

250942

AF XY:

0.169

show subpopulations

Gnomad AFR exome

AF:

0.193

Gnomad AMR exome

AF:

0.258

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.0123

Gnomad FIN exome

AF:

0.208

Gnomad NFE exome

AF:

0.205

Gnomad OTH exome

AF:

0.180

GnomAD4 exome

AF:

0.203

AC:

237722

AN:

1172284

Hom.:

26494

Cov.:

AF XY:

0.196

AC XY:

117023

AN XY:

595890

show subpopulations

African (AFR)

AF:

0.197

AC:

5451

AN:

27666

American (AMR)

AF:

0.255

AC:

11258

AN:

44104

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

3962

AN:

24292

East Asian (EAS)

AF:

0.0172

AC:

654

AN:

38088

South Asian (SAS)

AF:

0.0615

AC:

4907

AN:

79726

European-Finnish (FIN)

AF:

0.212

AC:

11121

AN:

52546

Middle Eastern (MID)

AF:

0.102

AC:

369

AN:

3628

European-Non Finnish (NFE)

AF:

0.224

AC:

190629

AN:

852034

Other (OTH)

AF:

0.187

AC:

9371

AN:

50200

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.554

Heterozygous variant carriers

11263

22525

33788

45050

56313

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5886

11772

17658

23544

29430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.186

AC:

28350

AN:

152118

Hom.:

2810

Cov.:

AF XY:

0.181

AC XY:

13459

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.186

AC:

7715

AN:

41478

American (AMR)

AF:

0.206

AC:

3149

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

564

AN:

3466

East Asian (EAS)

AF:

0.0135

AC:

AN:

5174

South Asian (SAS)

AF:

0.0530

AC:

256

AN:

4826

European-Finnish (FIN)

AF:

0.195

AC:

2058

AN:

10574

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

14024

AN:

67998

Other (OTH)

AF:

0.168

AC:

354

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1177

2355

3532

4710

5887

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

304

608

912

1216

1520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.200

Hom.:

603

Bravo

AF:

0.190

Asia WGS

AF:

0.0510

AC:

181

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.9

(source)

DANN

Benign

0.79

PhyloP100

-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over