chr1-165118255-G-A

Variant names:

• chr1-165118255-G-A
• rs2172712

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 0.441 in 151,832 control chromosomes in the GnomAD database, including 15,264 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 0.44 (15264 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.67 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: 0.441 AC: 66920 AN: 151712 Hom.: 15250 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.441 AC: 66974 AN: 151832 Hom.: 15264 Cov.: 31 AF XY: 0.446 AC XY: 33112 AN XY: 74174

African (AFR) AF: 0.385 AC: 15925 AN: 41388

American (AMR) AF: 0.405 AC: 6191 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1602 AN: 3464

East Asian (EAS) AF: 0.688 AC: 3543 AN: 5146

South Asian (SAS) AF: 0.517 AC: 2482 AN: 4800

European-Finnish (FIN) AF: 0.548 AC: 5765 AN: 10516

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30137 AN: 67936

Other (OTH) AF: 0.427 AC: 901 AN: 2110

Alfa AF: 0.431 Hom.: 41548

Bravo AF: 0.426

Asia WGS AF: 0.571 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.64
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2172712; hg19: chr1-165087492;