rs6508497

Variant names:

• chr18-27684377-C-T
• rs6508497

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.280

Alfa AF: 0.280 Hom.: 9213

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6508497; hg19: chr18-25264341;