rs6501455

Positions:

• chr17-71205670-A-G
• chr17-71205670-A-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 0.394 in 152,052 control chromosomes in the GnomAD database, including 12,366 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 0.39 (12366 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59952 AN: 151934 Hom.: 12359 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.394 AC: 59984 AN: 152052 Hom.: 12366 Cov.: 31 AF XY: 0.386 AC XY: 28695 AN XY: 74334

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.379

Alfa AF: 0.450 Hom.: 22098

Bravo AF: 0.395

Asia WGS AF: 0.322 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6501455; hg19: chr17-69201811;