dbSNP rs9725031: ENSG00000305110:n.374+4013G>A (chr1-232308709-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 ENST00000808822.1(ENSG00000305110):n.374+4013G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,176 control chromosomes in the GnomAD database, including 1,287 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 0.13 ( 1287 hom., cov: 32)

Consequence

ENSG00000305110
ENST00000808822.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.547

Publications

3 publications found

Variant links:

Genes affected

ENSG00000305110 (HGNC:):

ENSG00000305110 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929902	XR_001738524.2 link	n.711+4013G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305110	ENST00000808822.1 link	n.374+4013G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19293

AN:

152058

Hom.:

1285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.0767

Gnomad EAS

AF:

0.0725

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.123

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.127

AC:

19310

AN:

152176

Hom.:

1287

Cov.:

AF XY:

0.127

AC XY:

9424

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.169

AC:

6995

AN:

41508

American (AMR)

AF:

0.117

AC:

1783

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0767

AC:

266

AN:

3470

East Asian (EAS)

AF:

0.0724

AC:

375

AN:

5176

South Asian (SAS)

AF:

0.128

AC:

618

AN:

4816

European-Finnish (FIN)

AF:

0.119

AC:

1263

AN:

10582

Middle Eastern (MID)

AF:

0.116

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.113

AC:

7685

AN:

68010

Other (OTH)

AF:

0.123

AC:

260

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

863

1726

2588

3451

4314

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

214

428

642

856

1070

<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:

0.119

Hom.:

430

Bravo

AF:

0.126

Asia WGS

AF:

0.129

AC:

447

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

(source)

DANN

Benign

0.69

PhyloP100

-0.55

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over