rs4865656

Variant names:

• chr5-51363954-G-A
• rs4865656

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 0.441 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.441 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

African (AFR) AF: 0.640 AC: 26519 AN: 41432

American (AMR) AF: 0.376 AC: 5742 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1011 AN: 3470

East Asian (EAS) AF: 0.169 AC: 874 AN: 5180

South Asian (SAS) AF: 0.314 AC: 1512 AN: 4810

European-Finnish (FIN) AF: 0.377 AC: 3978 AN: 10558

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 26083 AN: 67980

Other (OTH) AF: 0.404 AC: 853 AN: 2110

Alfa AF: 0.395 Hom.: 23522

Bravo AF: 0.449

Asia WGS AF: 0.305 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.19
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4865656; hg19: chr5-50659788;