11-13151412-A-C

Variant names:

• chr11-13151412-A-C
• rs3860194

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 0.441 in 152,014 control chromosomes in the GnomAD database, including 16,565 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 0.44 (16565 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 4 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.554 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: 0.441 AC: 67009 AN: 151896 Hom.: 16564 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.441 AC: 67033 AN: 152014 Hom.: 16565 Cov.: 31 AF XY: 0.439 AC XY: 32607 AN XY: 74312

African (AFR) AF: 0.201 AC: 8339 AN: 41492

American (AMR) AF: 0.499 AC: 7620 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1714 AN: 3468

East Asian (EAS) AF: 0.375 AC: 1928 AN: 5148

South Asian (SAS) AF: 0.393 AC: 1888 AN: 4806

European-Finnish (FIN) AF: 0.560 AC: 5918 AN: 10570

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37949 AN: 67936

Other (OTH) AF: 0.461 AC: 970 AN: 2106

Alfa AF: 0.496 Hom.: 10482

Bravo AF: 0.430

Asia WGS AF: 0.343 AC: 1196 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	3.8
DANN	Benign	0.71
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs3860194; hg19: chr11-13172959;