11-15316438-C-T

Variant names:

• chr11-15316438-C-T
• rs4497390

Variant summary

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

The variant allele was found at a frequency of 0.69 in 152,082 control chromosomes in the GnomAD database, including 36,361 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 0.69 (36361 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104956 AN: 151964 Hom.: 36352 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.690 AC: 105007 AN: 152082 Hom.: 36361 Cov.: 33 AF XY: 0.692 AC XY: 51399 AN XY: 74318

African (AFR) AF: 0.683 AC: 28343 AN: 41472

American (AMR) AF: 0.699 AC: 10687 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2369 AN: 3468

East Asian (EAS) AF: 0.831 AC: 4294 AN: 5168

South Asian (SAS) AF: 0.640 AC: 3086 AN: 4822

European-Finnish (FIN) AF: 0.706 AC: 7456 AN: 10566

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

European-Non Finnish (NFE) AF: 0.683 AC: 46467 AN: 67992

Other (OTH) AF: 0.697 AC: 1470 AN: 2110

Alfa AF: 0.695 Hom.: 4763

Bravo AF: 0.693

Asia WGS AF: 0.723 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.73
DANN	Benign	0.74
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs4497390; hg19: chr11-15337984;