ENST00000380259.7:n.*739+51050G>T

Variant names:

• chr11-5539775-C-A
• rs10500648
• ENST00000380259.7:n.*739+51050G>T

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+51050G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,572 control chromosomes in the GnomAD database, including 22,546 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 0.53 (22546 hom., cov: 29)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 0 publications found

Genes affected

ENSG00000239920 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 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
ENSG00000239920	ENST00000380259.7	n.*739+51050G>T		intron_variant	Intron 5 of 7	5		ENSP00000369609.3

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80721 AN: 151452 Hom.: 22537 Cov.: 29

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.0846

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.533 AC: 80779 AN: 151572 Hom.: 22546 Cov.: 29 AF XY: 0.527 AC XY: 39019 AN XY: 74022

African (AFR) AF: 0.461 AC: 19020 AN: 41252

American (AMR) AF: 0.534 AC: 8125 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3468

East Asian (EAS) AF: 0.0850 AC: 438 AN: 5152

South Asian (SAS) AF: 0.363 AC: 1746 AN: 4808

European-Finnish (FIN) AF: 0.603 AC: 6316 AN: 10478

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41617 AN: 67920

Other (OTH) AF: 0.521 AC: 1087 AN: 2088

Alfa AF: 0.561 Hom.: 11045

Bravo AF: 0.518

Asia WGS AF: 0.236 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.72
DANN	Benign	0.60
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10500648; hg19: chr11-5561005; COSMIC: COSV59505499;