22-37585722-T-C

Variant names:

• chr22-37585722-T-C
• rs5995472

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 0.628 in 151,924 control chromosomes in the GnomAD database, including 30,466 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 0.63 (30466 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 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: 0.627 AC: 95243 AN: 151806 Hom.: 30421 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.628 AC: 95346 AN: 151924 Hom.: 30466 Cov.: 31 AF XY: 0.630 AC XY: 46795 AN XY: 74244

African (AFR) AF: 0.731 AC: 30266 AN: 41416

American (AMR) AF: 0.671 AC: 10229 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2298 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2479 AN: 5160

South Asian (SAS) AF: 0.594 AC: 2858 AN: 4812

European-Finnish (FIN) AF: 0.623 AC: 6570 AN: 10548

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38600 AN: 67948

Other (OTH) AF: 0.628 AC: 1327 AN: 2112

Alfa AF: 0.590 Hom.: 34613

Bravo AF: 0.638

Asia WGS AF: 0.542 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.33
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs5995472; hg19: chr22-37981729; COSMIC: COSV107521326;