11-636784-T-C

Variant names:

• chr11-636784-T-C
• rs1800955

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 0.427 in 147,208 control chromosomes in the GnomAD database, including 13,621 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 0.43 (13621 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 231 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.427 AC: 62856 AN: 147106 Hom.: 13615 Cov.: 26

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.427 AC: 62895 AN: 147208 Hom.: 13621 Cov.: 26 AF XY: 0.426 AC XY: 30532 AN XY: 71648

African (AFR) AF: 0.400 AC: 15816 AN: 39538

American (AMR) AF: 0.390 AC: 5781 AN: 14834

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1874 AN: 3432

East Asian (EAS) AF: 0.384 AC: 1854 AN: 4830

South Asian (SAS) AF: 0.427 AC: 1969 AN: 4616

European-Finnish (FIN) AF: 0.425 AC: 4188 AN: 9862

Middle Eastern (MID) AF: 0.469 AC: 135 AN: 288

European-Non Finnish (NFE) AF: 0.450 AC: 30088 AN: 66906

Other (OTH) AF: 0.461 AC: 935 AN: 2028

Alfa AF: 0.437 Hom.: 3785

Bravo AF: 0.423

Asia WGS AF: 0.403 AC: 1400 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.41
PhyloP100		-0.56
PromoterAI		0.012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1800955; hg19: chr11-636784; COSMIC: COSV51563474;