Genetic Variant ENSG00000256723: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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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