rs719737

Variant names:

• chr13-109698002-T-C
• rs719737
• ENST00000650264.1:n.758+32941A>G

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.758+32941A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 151,926 control chromosomes in the GnomAD database, including 1,505 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 0.14 (1505 hom., cov: 32)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 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
ENSG00000285534	ENST00000650264.1	n.758+32941A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20745 AN: 151808 Hom.: 1508 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.137 AC: 20755 AN: 151926 Hom.: 1505 Cov.: 32 AF XY: 0.134 AC XY: 9979 AN XY: 74252

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0998

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.147

Alfa AF: 0.138 Hom.: 2966

Bravo AF: 0.136

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719737; hg19: chr13-110350349;