rs4865656

Positions:

• chr5-51363954-G-A

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 0.441 in 152,026 control chromosomes in the GnomAD database, including 16,185 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 0.44 (16185 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 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: 0.441 AC: 66923 AN: 151908 Hom.: 16153 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.441 AC: 67001 AN: 152026 Hom.: 16185 Cov.: 33 AF XY: 0.433 AC XY: 32152 AN XY: 74314

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.404

Alfa AF: 0.386 Hom.: 15839

Bravo AF: 0.449

Asia WGS AF: 0.305 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4865656; hg19: chr5-50659788;