rs3761738

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000247372 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000501886.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000247372	ENST00000501886.2	TSL:4	n.107-276G>A		intron	N/A
	ENSG00000303479	ENST00000794888.1		n.*85C>T		downstream_gene	N/A

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

African (AFR) AF: 0.0325 AC: 1350 AN: 41564

American (AMR) AF: 0.116 AC: 1768 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3470

East Asian (EAS) AF: 0.0270 AC: 140 AN: 5192

South Asian (SAS) AF: 0.121 AC: 583 AN: 4820

European-Finnish (FIN) AF: 0.111 AC: 1174 AN: 10590

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0976 AC: 6636 AN: 68018

Other (OTH) AF: 0.0701 AC: 148 AN: 2112

Alfa AF: 0.0911 Hom.: 1146

Bravo AF: 0.0765

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.50
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs3761738; hg19: chr5-74631139;