dbSNP rs1150895: ENSG00000308473:n.154+1972A>G (chr1-226868390-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000834471.1(ENSG00000308473):n.154+1972A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,228 control chromosomes in the GnomAD database, including 2,278 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 0.15 ( 2278 hom., cov: 32)

Consequence

ENSG00000308473
ENST00000834471.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.538

Publications

3 publications found

Variant links:

Genes affected

ENSG00000308473 (HGNC:):

ENSG00000308473 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373119	XR_949226.4 link	n.189+1972A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308473	ENST00000834471.1 link	n.154+1972A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23588

AN:

152110

Hom.:

2276

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0444

Gnomad AMI

AF:

0.256

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.173

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.204

Gnomad OTH

AF:

0.170

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

GnomAD4 genome

AF:

0.155

AC:

23586

AN:

152228

Hom.:

2278

Cov.:

AF XY:

0.155

AC XY:

11504

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0444

AC:

1845

AN:

41560

American (AMR)

AF:

0.185

AC:

2822

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

714

AN:

3466

East Asian (EAS)

AF:

0.248

AC:

1285

AN:

5186

South Asian (SAS)

AF:

0.172

AC:

831

AN:

4824

European-Finnish (FIN)

AF:

0.148

AC:

1569

AN:

10578

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.204

AC:

13879

AN:

68010

Other (OTH)

AF:

0.170

AC:

359

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1031

2062

3093

4124

5155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.190

Hom.:

1453

Bravo

AF:

0.148

Asia WGS

AF:

0.182

AC:

635

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.7

(source)

DANN

Benign

0.67

PhyloP100

0.54

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