rs4911642

Positions:

• chr22-15473564-G-A
• chr22-15473564-G-C
• chr22-15473564-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.512).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.725

Alfa AF: 0.845 Hom.: 22988

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.51
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4911642; hg19: -;