rs6501384

Variant names:

• chr17-70294992-C-T
• rs6501384

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 0.342 in 151,932 control chromosomes in the GnomAD database, including 9,045 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 0.34 (9045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 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: 0.342 AC: 51989 AN: 151814 Hom.: 9037 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.342 AC: 52030 AN: 151932 Hom.: 9045 Cov.: 32 AF XY: 0.340 AC XY: 25240 AN XY: 74262

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.356

Alfa AF: 0.344 Hom.: 20986

Bravo AF: 0.339

Asia WGS AF: 0.337 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6501384; hg19: chr17-68291133;