rs3761739

chr5-75335676-C-T

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, non coding transcript 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: ENST00000501886.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000501886.2	n.107-638G>A		intron_variant, non_coding_transcript_variant		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;