22-31959468-T-C

Variant names:

• chr22-31959468-T-C
• rs5998196

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 0.516 in 152,140 control chromosomes in the GnomAD database, including 22,547 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 0.52 (22547 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78431 AN: 152022 Hom.: 22491 Cov.: 33

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.516 AC: 78543 AN: 152140 Hom.: 22547 Cov.: 33 AF XY: 0.508 AC XY: 37818 AN XY: 74374

African (AFR) AF: 0.782 AC: 32446 AN: 41510

American (AMR) AF: 0.443 AC: 6766 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1003 AN: 5182

South Asian (SAS) AF: 0.389 AC: 1876 AN: 4824

European-Finnish (FIN) AF: 0.383 AC: 4050 AN: 10572

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29437 AN: 67998

Other (OTH) AF: 0.465 AC: 983 AN: 2114

Alfa AF: 0.465 Hom.: 51042

Bravo AF: 0.530

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs5998196; hg19: chr22-32355455;