rs6508497

Variant names:

• chr18-27684377-C-T
• rs6508497

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 0.299 in 152,076 control chromosomes in the GnomAD database, including 6,957 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 0.30 (6957 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 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: 0.299 AC: 45483 AN: 151958 Hom.: 6953 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.299 AC: 45526 AN: 152076 Hom.: 6957 Cov.: 33 AF XY: 0.305 AC XY: 22652 AN XY: 74336

African (AFR) AF: 0.321 AC: 13314 AN: 41478

American (AMR) AF: 0.287 AC: 4388 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1342 AN: 5158

South Asian (SAS) AF: 0.430 AC: 2073 AN: 4818

European-Finnish (FIN) AF: 0.341 AC: 3603 AN: 10558

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18818 AN: 68008

Other (OTH) AF: 0.280 AC: 591 AN: 2110

Alfa AF: 0.282 Hom.: 23073

Bravo AF: 0.291

Asia WGS AF: 0.383 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.038
DANN	Benign	0.50
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6508497; hg19: chr18-25264341;