22-27267682-T-C

Variant names:

• chr22-27267682-T-C
• rs4412

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 0.661 in 152,074 control chromosomes in the GnomAD database, including 34,785 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 0.66 (34785 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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: 0.660 AC: 100320 AN: 151956 Hom.: 34718 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.661 AC: 100450 AN: 152074 Hom.: 34785 Cov.: 32 AF XY: 0.665 AC XY: 49394 AN XY: 74320

African (AFR) AF: 0.877 AC: 36424 AN: 41546

American (AMR) AF: 0.670 AC: 10241 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3466

East Asian (EAS) AF: 0.711 AC: 3674 AN: 5164

South Asian (SAS) AF: 0.708 AC: 3403 AN: 4808

European-Finnish (FIN) AF: 0.592 AC: 6253 AN: 10558

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36464 AN: 67940

Other (OTH) AF: 0.643 AC: 1356 AN: 2110

Alfa AF: 0.572 Hom.: 44558

Bravo AF: 0.675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.031
DANN	Benign	0.53
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4412; hg19: chr22-27663643; COSMIC: COSV53892229;