11-13272358-C-T

Variant names:

• chr11-13272358-C-T
• rs900145

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 0.62 in 152,134 control chromosomes in the GnomAD database, including 30,117 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 0.62 (30117 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 60 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.620 AC: 94213 AN: 152016 Hom.: 30084 Cov.: 34

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.620 AC: 94299 AN: 152134 Hom.: 30117 Cov.: 34 AF XY: 0.622 AC XY: 46291 AN XY: 74374

African (AFR) AF: 0.463 AC: 19213 AN: 41464

American (AMR) AF: 0.618 AC: 9451 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2295 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2781 AN: 5188

South Asian (SAS) AF: 0.637 AC: 3076 AN: 4828

European-Finnish (FIN) AF: 0.723 AC: 7639 AN: 10560

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47760 AN: 68008

Other (OTH) AF: 0.640 AC: 1354 AN: 2114

Alfa AF: 0.678 Hom.: 121153

Bravo AF: 0.607

Asia WGS AF: 0.605 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.53
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs900145; hg19: chr11-13293905;