ENST00000380259.7:n.*739+13191A>C

Variant names:

• chr11-5577634-T-G
• rs4910571
• ENST00000380259.7:n.*739+13191A>C

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+13191A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,880 control chromosomes in the GnomAD database, including 14,049 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 0.41 (14049 hom., cov: 31)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 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+13191A>C		intron_variant	Intron 5 of 7	5		ENSP00000369609.3
ENSG00000239920	ENST00000394793.3	n.256-5035A>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62532 AN: 151762 Hom.: 14026 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.412 AC: 62604 AN: 151880 Hom.: 14049 Cov.: 31 AF XY: 0.421 AC XY: 31250 AN XY: 74206

African (AFR) AF: 0.514 AC: 21269 AN: 41402

American (AMR) AF: 0.523 AC: 7966 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3470

East Asian (EAS) AF: 0.751 AC: 3885 AN: 5170

South Asian (SAS) AF: 0.502 AC: 2421 AN: 4826

European-Finnish (FIN) AF: 0.347 AC: 3654 AN: 10528

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20855 AN: 67936

Other (OTH) AF: 0.407 AC: 859 AN: 2108

Alfa AF: 0.347 Hom.: 15977

Bravo AF: 0.434

Asia WGS AF: 0.604 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.83
PhyloP100		-0.52
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: rs4910571; hg19: chr11-5598864;