rs3761738

Variant names:

• chr5-75335314-C-T
• rs3761738
• ENST00000501886.2:n.107-276G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000501886.2(ENSG00000247372):​n.107-276G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,270 control chromosomes in the GnomAD database, including 595 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 0.082 (595 hom., cov: 32)
• Consequence: ENSG00000247372 ENST00000501886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

ENSG00000247372 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 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
ENSG00000247372	ENST00000501886.2	n.107-276G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12441 AN: 152152 Hom.: 594 Cov.: 32

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0976

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0817 AC: 12437 AN: 152270 Hom.: 595 Cov.: 32 AF XY: 0.0830 AC XY: 6178 AN XY: 74456

Gnomad4 AFR AF: 0.0325

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0270

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0976

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0950 Hom.: 719

Bravo AF: 0.0765

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761738; hg19: chr5-74631139;