rs5757463

chr22-39076560-G-Cchr22-39076560-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.918

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.935

Gnomad4 OTH AF: 0.935

Alfa AF: 0.932 Hom.: 2944

Bravo AF: 0.931

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.88
Dann	Benign	0.21

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

Publications

LitVar

Other links and lift over

dbSNP: rs5757463; hg19: chr22-39472565;