5-62949231-G-A

Variant names:

• chr5-62949231-G-A
• rs4446414

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 0.0191 in 152,218 control chromosomes in the GnomAD database, including 64 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 0.019 (64 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0191 AC: 2898 AN: 152100 Hom.: 63 Cov.: 32

Gnomad AFR AF: 0.0297

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00737

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0191 AC: 2911 AN: 152218 Hom.: 64 Cov.: 32 AF XY: 0.0195 AC XY: 1453 AN XY: 74420

African (AFR) AF: 0.0298 AC: 1238 AN: 41524

American (AMR) AF: 0.0149 AC: 228 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3470

East Asian (EAS) AF: 0.101 AC: 522 AN: 5174

South Asian (SAS) AF: 0.0675 AC: 325 AN: 4818

European-Finnish (FIN) AF: 0.00151 AC: 16 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00737 AC: 501 AN: 68014

Other (OTH) AF: 0.0194 AC: 41 AN: 2114

Alfa AF: 0.0124 Hom.: 3

Bravo AF: 0.0196

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.93
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs4446414; hg19: chr5-62245058;