11-2284938-C-T

Variant names:

• chr11-2284938-C-T
• rs7104786

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 0.41 in 151,944 control chromosomes in the GnomAD database, including 13,181 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 0.41 (13181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.548 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: 0.410 AC: 62246 AN: 151826 Hom.: 13166 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.410 AC: 62292 AN: 151944 Hom.: 13181 Cov.: 32 AF XY: 0.408 AC XY: 30288 AN XY: 74238

African (AFR) AF: 0.487 AC: 20160 AN: 41434

American (AMR) AF: 0.294 AC: 4488 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3464

East Asian (EAS) AF: 0.464 AC: 2404 AN: 5176

South Asian (SAS) AF: 0.566 AC: 2729 AN: 4822

European-Finnish (FIN) AF: 0.331 AC: 3483 AN: 10522

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26694 AN: 67960

Other (OTH) AF: 0.389 AC: 819 AN: 2106

Alfa AF: 0.386 Hom.: 26715

Bravo AF: 0.408

Asia WGS AF: 0.510 AC: 1775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.72
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs7104786; hg19: chr11-2306168;