11-5513952-A-C

Variant names:

• chr11-5513952-A-C
• rs934460
• ENST00000380259.7:n.*739+76873T>G

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+76873T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,094 control chromosomes in the GnomAD database, including 19,324 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 0.50 (19324 hom., cov: 33)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 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+76873T>G		intron_variant	Intron 5 of 7	5		ENSP00000369609.3

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75997 AN: 151976 Hom.: 19307 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.500 AC: 76053 AN: 152094 Hom.: 19324 Cov.: 33 AF XY: 0.508 AC XY: 37737 AN XY: 74350

African (AFR) AF: 0.461 AC: 19105 AN: 41462

American (AMR) AF: 0.550 AC: 8416 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3468

East Asian (EAS) AF: 0.658 AC: 3400 AN: 5168

South Asian (SAS) AF: 0.635 AC: 3066 AN: 4826

European-Finnish (FIN) AF: 0.564 AC: 5966 AN: 10586

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32690 AN: 67974

Other (OTH) AF: 0.504 AC: 1066 AN: 2116

Alfa AF: 0.348 Hom.: 932

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.023
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: rs934460; hg19: chr11-5535182;