rs4976360

Variant names:

• chr5-136018635-T-A
• rs4976360

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 0.427 in 152,012 control chromosomes in the GnomAD database, including 15,295 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 0.43 (15295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 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: 0.427 AC: 64860 AN: 151894 Hom.: 15297 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.427 AC: 64874 AN: 152012 Hom.: 15295 Cov.: 32 AF XY: 0.424 AC XY: 31483 AN XY: 74298

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.429

Alfa AF: 0.469 Hom.: 2160

Bravo AF: 0.410

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.9
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: rs4976360; hg19: chr5-135354324;