Genetic Variant ENST00000544832.1:n.906G>A (chr11-73995246-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000544832.1(ENSG00000256723):n.906G>A 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 0.223 in 156,904 control chromosomes in the GnomAD database, including 4,236 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 0.22 ( 4029 hom., cov: 32)

Exomes 𝑓: 0.29 ( 207 hom. )

Consequence

ENSG00000256723
ENST00000544832.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170

Publications

5 publications found

Variant links:

Genes affected

ENSG00000256723 (HGNC:):

ENSG00000256723 links:

Genome browser will be placed here

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=-0.62).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100421622		n.73995246C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256723	ENST00000544832.1 link	n.906G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33514

AN:

151948

Hom.:

4032

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.147

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.293

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.185

GnomAD4 exome

AF:

0.289

AC:

1399

AN:

4836

Hom.:

207

Cov.:

AF XY:

0.280

AC XY:

891

AN XY:

3180

show subpopulations

African (AFR)

AF:

0.155

AC:

AN:

American (AMR)

AF:

0.261

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.192

AC:

AN:

East Asian (EAS)

AF:

0.303

AC:

AN:

178

South Asian (SAS)

AF:

0.213

AC:

122

AN:

574

European-Finnish (FIN)

AF:

0.387

AC:

385

AN:

994

Middle Eastern (MID)

AF:

0.143

AC:

AN:

European-Non Finnish (NFE)

AF:

0.278

AC:

752

AN:

2704

Other (OTH)

AF:

0.252

AC:

AN:

202

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

149

198

248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.220

AC:

33516

AN:

152068

Hom.:

4029

Cov.:

AF XY:

0.225

AC XY:

16752

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.166

AC:

6893

AN:

41476

American (AMR)

AF:

0.147

AC:

2243

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

740

AN:

3472

East Asian (EAS)

AF:

0.293

AC:

1519

AN:

5178

South Asian (SAS)

AF:

0.241

AC:

1158

AN:

4810

European-Finnish (FIN)

AF:

0.381

AC:

4019

AN:

10554

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.241

AC:

16393

AN:

67980

Other (OTH)

AF:

0.184

AC:

389

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1337

2675

4012

5350

6687

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

360

720

1080

1440

1800

<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:

0.227

Hom.:

676

Bravo

AF:

0.197

Asia WGS

AF:

0.246

AC:

852

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

6.0

(source)

DANN

Benign

0.64

PhyloP100

-0.017

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over