rs6508497

Positions:

• chr18-27684377-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;