chr11-2184662-G-T

Variant names:

• chr11-2184662-G-T
• rs7396243

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 0.468 in 152,000 control chromosomes in the GnomAD database, including 19,460 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 0.47 (19460 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.469 AC: 71202 AN: 151882 Hom.: 19469 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.468 AC: 71193 AN: 152000 Hom.: 19460 Cov.: 32 AF XY: 0.477 AC XY: 35401 AN XY: 74286

African (AFR) AF: 0.168 AC: 6972 AN: 41438

American (AMR) AF: 0.465 AC: 7105 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1863 AN: 3458

East Asian (EAS) AF: 0.759 AC: 3917 AN: 5162

South Asian (SAS) AF: 0.671 AC: 3231 AN: 4818

European-Finnish (FIN) AF: 0.624 AC: 6597 AN: 10564

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39678 AN: 67968

Other (OTH) AF: 0.535 AC: 1125 AN: 2102

Alfa AF: 0.366 Hom.: 1222

Bravo AF: 0.445

Asia WGS AF: 0.670 AC: 2331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.093
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7396243; hg19: chr11-2205892;