22-39076169-C-G

Variant names:

• chr22-39076169-C-G
• rs7291971

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 0.473 in 151,690 control chromosomes in the GnomAD database, including 20,046 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 0.47 (20046 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.711 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: 0.473 AC: 71713 AN: 151570 Hom.: 20038 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.473 AC: 71718 AN: 151690 Hom.: 20046 Cov.: 31 AF XY: 0.475 AC XY: 35203 AN XY: 74122

African (AFR) AF: 0.150 AC: 6231 AN: 41448

American (AMR) AF: 0.638 AC: 9714 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2014 AN: 3458

East Asian (EAS) AF: 0.731 AC: 3748 AN: 5130

South Asian (SAS) AF: 0.588 AC: 2826 AN: 4806

European-Finnish (FIN) AF: 0.511 AC: 5353 AN: 10474

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40058 AN: 67832

Other (OTH) AF: 0.542 AC: 1142 AN: 2106

Alfa AF: 0.372 Hom.: 1134

Bravo AF: 0.471

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		0.055
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7291971; hg19: chr22-39472174;