chr22-15473564-G-A

Variant names:

• chr22-15473564-G-A
• rs4911642

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.72 (22965 hom., cov: 11)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.512).
• BS2: High Homozygotes in GnomAd4 at 22965 gene

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: 0.722 AC: 61117 AN: 84604 Hom.: 22963 Cov.: 11

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.722 AC: 61118 AN: 84606 Hom.: 22965 Cov.: 11 AF XY: 0.716 AC XY: 27794 AN XY: 38842

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.561 AC: 14209 AN: 25340

American (AMR) AF: 0.799 AC: 4928 AN: 6168

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 1880 AN: 2350

East Asian (EAS) AF: 0.760 AC: 2055 AN: 2704

South Asian (SAS) AF: 0.766 AC: 1590 AN: 2076

European-Finnish (FIN) AF: 0.664 AC: 1551 AN: 2336

Middle Eastern (MID) AF: 0.713 AC: 97 AN: 136

European-Non Finnish (NFE) AF: 0.802 AC: 33580 AN: 41878

Other (OTH) AF: 0.725 AC: 731 AN: 1008

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.847 Hom.: 33003

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.51
DANN	Benign	0.15
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs4911642;