ENST00000765862.1:n.409-13098C>T

Variant names:

• chr4-137661557-G-A
• rs17049741
• ENST00000765862.1:n.409-13098C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000765862.1(ENSG00000250126):​n.409-13098C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,176 control chromosomes in the GnomAD database, including 2,480 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 0.16 (2480 hom., cov: 32)
• Consequence: ENSG00000250126 ENST00000765862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 5 publications found

Genes affected

ENSG00000250126 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765862.1. 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
	LOC101927414	NR_187911.1		n.140-13098C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250126	ENST00000765862.1		n.409-13098C>T		intron	N/A
	ENSG00000250126	ENST00000765956.1		n.228-13098C>T		intron	N/A
	ENSG00000250126	ENST00000765957.1		n.200-6331C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23766 AN: 151058 Hom.: 2476 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.157 AC: 23771 AN: 151176 Hom.: 2480 Cov.: 32 AF XY: 0.158 AC XY: 11707 AN XY: 73960

African (AFR) AF: 0.0388 AC: 1578 AN: 40680

American (AMR) AF: 0.149 AC: 2269 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2211 AN: 5146

South Asian (SAS) AF: 0.249 AC: 1203 AN: 4824

European-Finnish (FIN) AF: 0.210 AC: 2215 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13347 AN: 67960

Other (OTH) AF: 0.153 AC: 321 AN: 2100

Alfa AF: 0.166 Hom.: 4567

Bravo AF: 0.145

Asia WGS AF: 0.309 AC: 1071 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.013
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17049741; hg19: chr4-138582711;