chr1-197015549-A-G

Variant names:

• chr1-197015549-A-G
• rs1332666

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 0.384 in 151,736 control chromosomes in the GnomAD database, including 12,795 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 0.38 (12795 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58190 AN: 151620 Hom.: 12786 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.384 AC: 58212 AN: 151736 Hom.: 12795 Cov.: 31 AF XY: 0.378 AC XY: 28003 AN XY: 74140

African (AFR) AF: 0.192 AC: 7935 AN: 41304

American (AMR) AF: 0.343 AC: 5238 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3468

East Asian (EAS) AF: 0.129 AC: 666 AN: 5166

South Asian (SAS) AF: 0.377 AC: 1813 AN: 4806

European-Finnish (FIN) AF: 0.456 AC: 4800 AN: 10518

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.511 AC: 34718 AN: 67908

Other (OTH) AF: 0.390 AC: 822 AN: 2108

Alfa AF: 0.507 Hom.: 21298

Bravo AF: 0.366

Asia WGS AF: 0.256 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.0
DANN	Benign	0.93
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1332666; hg19: chr1-196984679; COSMIC: COSV60014215;