chr5-50279343-A-C

Variant names:

• chr5-50279343-A-C
• rs4865676

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 0.605 in 151,862 control chromosomes in the GnomAD database, including 28,299 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 0.60 (28299 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 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: 0.605 AC: 91779 AN: 151744 Hom.: 28296 Cov.: 30

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.605 AC: 91817 AN: 151862 Hom.: 28299 Cov.: 30 AF XY: 0.609 AC XY: 45162 AN XY: 74204

African (AFR) AF: 0.489 AC: 20255 AN: 41424

American (AMR) AF: 0.640 AC: 9765 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2219 AN: 3468

East Asian (EAS) AF: 0.514 AC: 2633 AN: 5124

South Asian (SAS) AF: 0.619 AC: 2978 AN: 4812

European-Finnish (FIN) AF: 0.723 AC: 7630 AN: 10548

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.650 AC: 44165 AN: 67928

Other (OTH) AF: 0.634 AC: 1332 AN: 2100

Alfa AF: 0.583 Hom.: 3753

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.15
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4865676; hg19: chr5-49575177;