1-173068108-A-G

Variant names:

• chr1-173068108-A-G
• rs2223517

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 0.569 in 151,530 control chromosomes in the GnomAD database, including 24,990 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 0.57 (24990 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 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: 0.569 AC: 86217 AN: 151412 Hom.: 24969 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.569 AC: 86290 AN: 151530 Hom.: 24990 Cov.: 31 AF XY: 0.571 AC XY: 42288 AN XY: 74012

African (AFR) AF: 0.604 AC: 24992 AN: 41348

American (AMR) AF: 0.547 AC: 8307 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2142 AN: 3460

East Asian (EAS) AF: 0.844 AC: 4344 AN: 5148

South Asian (SAS) AF: 0.743 AC: 3575 AN: 4812

European-Finnish (FIN) AF: 0.498 AC: 5212 AN: 10472

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35724 AN: 67784

Other (OTH) AF: 0.592 AC: 1245 AN: 2104

Alfa AF: 0.551 Hom.: 16457

Bravo AF: 0.573

Asia WGS AF: 0.765 AC: 2659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.54
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2223517; hg19: chr1-173037248;