rs3761739

Variant names:

• chr5-75335676-C-T
• rs3761739
• ENST00000501886.2:n.107-638G>A

Variant summary

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

The ENST00000501886.2(ENSG00000247372):​n.107-638G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,970 control chromosomes in the GnomAD database, including 1,849 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 0.15 (1849 hom., cov: 31)
• Consequence: ENSG00000247372 ENST00000501886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

ENSG00000247372 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 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.107-638G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23169 AN: 151852 Hom.: 1845 Cov.: 31

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.153 AC: 23192 AN: 151970 Hom.: 1849 Cov.: 31 AF XY: 0.156 AC XY: 11559 AN XY: 74262

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.135

Alfa AF: 0.151 Hom.: 2449

Bravo AF: 0.151

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761739; hg19: chr5-74631501;