rs4302532

Variant names:

• chr5-63362844-T-C
• rs4302532

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 0.187 in 152,186 control chromosomes in the GnomAD database, including 3,180 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 0.19 (3180 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 5 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 = 0.292 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: 0.187 AC: 28447 AN: 152070 Hom.: 3172 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0765

Gnomad FIN AF: 0.0810

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.187 AC: 28489 AN: 152186 Hom.: 3180 Cov.: 33 AF XY: 0.179 AC XY: 13350 AN XY: 74408

African (AFR) AF: 0.296 AC: 12293 AN: 41510

American (AMR) AF: 0.167 AC: 2558 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 776 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5174

South Asian (SAS) AF: 0.0770 AC: 372 AN: 4830

European-Finnish (FIN) AF: 0.0810 AC: 859 AN: 10606

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10929 AN: 67986

Other (OTH) AF: 0.226 AC: 478 AN: 2116

Alfa AF: 0.175 Hom.: 1098

Bravo AF: 0.202

Asia WGS AF: 0.0650 AC: 229 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.45
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4302532; hg19: chr5-62658671;