22-39076560-G-C

Variant names:

• chr22-39076560-G-C
• rs5757463

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 0.93 in 152,246 control chromosomes in the GnomAD database, including 65,938 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 0.93 (65938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.944 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: 0.930 AC: 141540 AN: 152128 Hom.: 65899 Cov.: 32

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.930 AC: 141636 AN: 152246 Hom.: 65938 Cov.: 32 AF XY: 0.931 AC XY: 69309 AN XY: 74430

African (AFR) AF: 0.910 AC: 37786 AN: 41534

American (AMR) AF: 0.957 AC: 14651 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3283 AN: 3470

East Asian (EAS) AF: 0.898 AC: 4646 AN: 5176

South Asian (SAS) AF: 0.918 AC: 4421 AN: 4818

European-Finnish (FIN) AF: 0.952 AC: 10101 AN: 10614

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63600 AN: 68012

Other (OTH) AF: 0.935 AC: 1972 AN: 2110

Alfa AF: 0.932 Hom.: 2944

Bravo AF: 0.931

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.88
DANN	Benign	0.21
PhyloP100		-2.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs5757463; hg19: chr22-39472565;