1-161741462-A-G

Variant names:

• chr1-161741462-A-G
• rs1340981

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 0.512 in 151,472 control chromosomes in the GnomAD database, including 22,985 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 0.51 (22985 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 5 publications found

ACMG classification

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 = 0.815 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: 0.511 AC: 77404 AN: 151354 Hom.: 22944 Cov.: 30

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.512 AC: 77491 AN: 151472 Hom.: 22985 Cov.: 30 AF XY: 0.507 AC XY: 37543 AN XY: 74010

African (AFR) AF: 0.822 AC: 33982 AN: 41340

American (AMR) AF: 0.376 AC: 5725 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3468

East Asian (EAS) AF: 0.700 AC: 3590 AN: 5130

South Asian (SAS) AF: 0.388 AC: 1863 AN: 4806

European-Finnish (FIN) AF: 0.368 AC: 3848 AN: 10460

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25825 AN: 67754

Other (OTH) AF: 0.470 AC: 984 AN: 2094

Alfa AF: 0.444 Hom.: 2915

Bravo AF: 0.524

Asia WGS AF: 0.518 AC: 1799 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.79
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1340981; hg19: chr1-161711252;