chr1-172482947-A-G

Variant names:

• chr1-172482947-A-G
• rs2032528

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.681 in 151,988 control chromosomes in the GnomAD database, including 35,532 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 0.68 (35532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103379 AN: 151870 Hom.: 35509 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.681 AC: 103449 AN: 151988 Hom.: 35532 Cov.: 32 AF XY: 0.680 AC XY: 50498 AN XY: 74280

African (AFR) AF: 0.658 AC: 27265 AN: 41414

American (AMR) AF: 0.739 AC: 11291 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2701 AN: 3472

East Asian (EAS) AF: 0.880 AC: 4549 AN: 5170

South Asian (SAS) AF: 0.764 AC: 3669 AN: 4804

European-Finnish (FIN) AF: 0.555 AC: 5856 AN: 10552

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45746 AN: 67970

Other (OTH) AF: 0.697 AC: 1474 AN: 2114

Alfa AF: 0.679 Hom.: 23289

Bravo AF: 0.694

Asia WGS AF: 0.806 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2032528; hg19: chr1-172452087;