rs682457

Variant names:

• chr11-88216364-T-C
• rs682457

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 0.139 in 152,196 control chromosomes in the GnomAD database, including 1,644 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 0.14 (1644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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: 0.139 AC: 21180 AN: 152078 Hom.: 1645 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.0797

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.139 AC: 21189 AN: 152196 Hom.: 1644 Cov.: 32 AF XY: 0.134 AC XY: 9979 AN XY: 74412

African (AFR) AF: 0.107 AC: 4452 AN: 41554

American (AMR) AF: 0.108 AC: 1655 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3472

East Asian (EAS) AF: 0.0236 AC: 122 AN: 5174

South Asian (SAS) AF: 0.0792 AC: 382 AN: 4826

European-Finnish (FIN) AF: 0.103 AC: 1094 AN: 10606

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11966 AN: 67992

Other (OTH) AF: 0.160 AC: 338 AN: 2112

Alfa AF: 0.154 Hom.: 728

Bravo AF: 0.140

Asia WGS AF: 0.0690 AC: 243 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs682457; hg19: chr11-87949532;