rs4302532

Positions:

• chr5-63362844-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0770

Gnomad4 FIN AF: 0.0810

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.226

Alfa AF: 0.171 Hom.: 838

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4302532; hg19: chr5-62658671;