chr11-118680047-T-C

Variant names:

• chr11-118680047-T-C
• rs642530

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 0.347 in 152,118 control chromosomes in the GnomAD database, including 9,462 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 0.35 (9462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 12 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 (AMR) allele frequency at 95% confidence interval = 0.464 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: 0.347 AC: 52712 AN: 152000 Hom.: 9440 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.347 AC: 52778 AN: 152118 Hom.: 9462 Cov.: 32 AF XY: 0.346 AC XY: 25701 AN XY: 74368

African (AFR) AF: 0.342 AC: 14170 AN: 41492

American (AMR) AF: 0.473 AC: 7225 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2290 AN: 5154

South Asian (SAS) AF: 0.197 AC: 949 AN: 4824

European-Finnish (FIN) AF: 0.313 AC: 3317 AN: 10590

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22272 AN: 67992

Other (OTH) AF: 0.351 AC: 740 AN: 2108

Alfa AF: 0.355 Hom.: 2104

Bravo AF: 0.366

Asia WGS AF: 0.304 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.76
PhyloP100		0.12
PromoterAI		-0.024	Neutral

Splicing

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

Other links and lift over

dbSNP: rs642530; hg19: chr11-118550756;