rs719737

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650264.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285534	ENST00000650264.1		n.758+32941A>G		intron	N/A

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

African (AFR) AF: 0.144 AC: 5971 AN: 41398

American (AMR) AF: 0.115 AC: 1760 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3468

East Asian (EAS) AF: 0.155 AC: 801 AN: 5152

South Asian (SAS) AF: 0.138 AC: 667 AN: 4818

European-Finnish (FIN) AF: 0.0998 AC: 1054 AN: 10558

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9321 AN: 67958

Other (OTH) AF: 0.147 AC: 311 AN: 2112

Alfa AF: 0.137 Hom.: 4427

Bravo AF: 0.136

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.76
PhyloP100		0.022

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs719737;

hg19: chr13-110350349;