rs2660917

Variant names:

• chr18-70960842-T-C
• rs2660917

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 0.259 in 151,994 control chromosomes in the GnomAD database, including 5,371 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 0.26 (5371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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: 0.259 AC: 39319 AN: 151876 Hom.: 5360 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.259 AC: 39359 AN: 151994 Hom.: 5371 Cov.: 32 AF XY: 0.256 AC XY: 19005 AN XY: 74286

African (AFR) AF: 0.304 AC: 12585 AN: 41464

American (AMR) AF: 0.191 AC: 2913 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3464

East Asian (EAS) AF: 0.0938 AC: 485 AN: 5172

South Asian (SAS) AF: 0.335 AC: 1614 AN: 4816

European-Finnish (FIN) AF: 0.243 AC: 2557 AN: 10534

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17692 AN: 67958

Other (OTH) AF: 0.230 AC: 484 AN: 2106

Alfa AF: 0.247 Hom.: 12284

Bravo AF: 0.250

Asia WGS AF: 0.228 AC: 786 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.72
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs2660917; hg19: chr18-68628078;