chr1-209815925-A-G

Variant names:

• chr1-209815925-A-G
• rs642961

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 0.834 in 152,080 control chromosomes in the GnomAD database, including 52,996 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 0.83 (52996 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778
• Publications: 130 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126679 AN: 151962 Hom.: 52956 Cov.: 30

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.834 AC: 126777 AN: 152080 Hom.: 52996 Cov.: 30 AF XY: 0.831 AC XY: 61744 AN XY: 74326

African (AFR) AF: 0.898 AC: 37249 AN: 41488

American (AMR) AF: 0.840 AC: 12852 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2819 AN: 3472

East Asian (EAS) AF: 0.809 AC: 4172 AN: 5158

South Asian (SAS) AF: 0.785 AC: 3776 AN: 4808

European-Finnish (FIN) AF: 0.777 AC: 8215 AN: 10566

Middle Eastern (MID) AF: 0.832 AC: 243 AN: 292

European-Non Finnish (NFE) AF: 0.808 AC: 54903 AN: 67982

Other (OTH) AF: 0.835 AC: 1762 AN: 2110

Alfa AF: 0.814 Hom.: 190205

Bravo AF: 0.839

Asia WGS AF: 0.766 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	14
DANN	Benign	0.62
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs642961; hg19: chr1-209989270;