11-27315157-C-T

Variant names:

• chr11-27315157-C-T
• rs10160456

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 0.6 in 152,044 control chromosomes in the GnomAD database, including 27,578 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 0.60 (27578 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.687 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: 0.600 AC: 91158 AN: 151926 Hom.: 27551 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.600 AC: 91233 AN: 152044 Hom.: 27578 Cov.: 33 AF XY: 0.596 AC XY: 44301 AN XY: 74328

African (AFR) AF: 0.586 AC: 24320 AN: 41476

American (AMR) AF: 0.698 AC: 10659 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2015 AN: 3468

East Asian (EAS) AF: 0.494 AC: 2553 AN: 5170

South Asian (SAS) AF: 0.639 AC: 3079 AN: 4820

European-Finnish (FIN) AF: 0.488 AC: 5158 AN: 10576

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41437 AN: 67942

Other (OTH) AF: 0.614 AC: 1297 AN: 2114

Alfa AF: 0.564 Hom.: 5810

Bravo AF: 0.618

Asia WGS AF: 0.599 AC: 2081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs10160456; hg19: chr11-27336704;