5-163502352-A-T

Variant names:

• chr5-163502352-A-T
• rs10462941

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 0.24 in 152,084 control chromosomes in the GnomAD database, including 5,886 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 0.24 (5886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36443 AN: 151966 Hom.: 5879 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.240 AC: 36464 AN: 152084 Hom.: 5886 Cov.: 32 AF XY: 0.248 AC XY: 18436 AN XY: 74324

African (AFR) AF: 0.105 AC: 4362 AN: 41502

American (AMR) AF: 0.377 AC: 5753 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3871 AN: 5170

South Asian (SAS) AF: 0.435 AC: 2099 AN: 4824

European-Finnish (FIN) AF: 0.236 AC: 2490 AN: 10544

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15767 AN: 67986

Other (OTH) AF: 0.266 AC: 561 AN: 2112

Alfa AF: 0.218 Hom.: 501

Bravo AF: 0.246

Asia WGS AF: 0.486 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.88
PhyloP100		0.90

Splicing

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

Publications

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Other links and lift over

dbSNP: rs10462941; hg19: chr5-162929358;