11-119831306-A-T

Variant names:

• chr11-119831306-A-T
• rs544201
• ENST00000813938.1:n.518+9715A>T

Variant summary

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

The ENST00000813938.1(ENSG00000287545):​n.518+9715A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,946 control chromosomes in the GnomAD database, including 32,705 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 0.65 (32705 hom., cov: 32)
• Consequence: ENSG00000287545 ENST00000813938.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 3 publications found

Genes affected

ENSG00000287545 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 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
ENSG00000287545	ENST00000813938.1	n.518+9715A>T		intron_variant	Intron 3 of 3
ENSG00000287545	ENST00000813939.1	n.310-1714A>T		intron_variant	Intron 2 of 3
ENSG00000287545	ENST00000813940.1	n.269-1714A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98289 AN: 151828 Hom.: 32682 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.647 AC: 98362 AN: 151946 Hom.: 32705 Cov.: 32 AF XY: 0.654 AC XY: 48604 AN XY: 74262

African (AFR) AF: 0.514 AC: 21283 AN: 41396

American (AMR) AF: 0.737 AC: 11264 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2584 AN: 3466

East Asian (EAS) AF: 0.954 AC: 4922 AN: 5160

South Asian (SAS) AF: 0.742 AC: 3573 AN: 4814

European-Finnish (FIN) AF: 0.697 AC: 7355 AN: 10554

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.667 AC: 45296 AN: 67956

Other (OTH) AF: 0.653 AC: 1376 AN: 2108

Alfa AF: 0.653 Hom.: 3886

Bravo AF: 0.643

Asia WGS AF: 0.815 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.77
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs544201; hg19: chr11-119702015;