22-19168604-T-C

Variant names:

• chr22-19168604-T-C
• rs712964

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 0.654 in 151,830 control chromosomes in the GnomAD database, including 33,219 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 0.65 (33219 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 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: 0.654 AC: 99204 AN: 151712 Hom.: 33164 Cov.: 30

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.654 AC: 99319 AN: 151830 Hom.: 33219 Cov.: 30 AF XY: 0.656 AC XY: 48676 AN XY: 74164

African (AFR) AF: 0.793 AC: 32859 AN: 41420

American (AMR) AF: 0.635 AC: 9686 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2017 AN: 3460

East Asian (EAS) AF: 0.513 AC: 2632 AN: 5128

South Asian (SAS) AF: 0.743 AC: 3569 AN: 4802

European-Finnish (FIN) AF: 0.606 AC: 6388 AN: 10538

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40107 AN: 67922

Other (OTH) AF: 0.633 AC: 1335 AN: 2108

Alfa AF: 0.610 Hom.: 87678

Bravo AF: 0.655

Asia WGS AF: 0.666 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.42
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs712964; hg19: chr22-19156117; COSMIC: COSV73767526;