rs642497

Variant names:

• chr11-118680075-C-A
• rs642497

Your query was ambiguous. Multiple possible variants found:

• chr11-118680075-C-A
• chr11-118680075-C-G

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 152,042 control chromosomes in the GnomAD database, including 9,435 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 (9435 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 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: 52649 AN: 151924 Hom.: 9413 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.327

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: 52715 AN: 152042 Hom.: 9435 Cov.: 31 AF XY: 0.345 AC XY: 25669 AN XY: 74338

African (AFR) AF: 0.341 AC: 14151 AN: 41464

American (AMR) AF: 0.472 AC: 7214 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2280 AN: 5148

South Asian (SAS) AF: 0.197 AC: 950 AN: 4830

European-Finnish (FIN) AF: 0.313 AC: 3312 AN: 10572

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

European-Non Finnish (NFE) AF: 0.327 AC: 22254 AN: 67976

Other (OTH) AF: 0.351 AC: 738 AN: 2104

Alfa AF: 0.330 Hom.: 7657

Bravo AF: 0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.47
PhyloP100		0.22
PromoterAI		-0.044	Neutral

Splicing

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

Other links and lift over

dbSNP: rs642497; hg19: chr11-118550784;