17-71205670-A-G

Variant names:

• chr17-71205670-A-G
• rs6501455

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 0.394 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.294 AC: 12214 AN: 41524

American (AMR) AF: 0.381 AC: 5823 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3468

East Asian (EAS) AF: 0.373 AC: 1927 AN: 5168

South Asian (SAS) AF: 0.274 AC: 1322 AN: 4826

European-Finnish (FIN) AF: 0.367 AC: 3870 AN: 10554

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32526 AN: 67928

Other (OTH) AF: 0.379 AC: 798 AN: 2108

Alfa AF: 0.451 Hom.: 29073

Bravo AF: 0.395

Asia WGS AF: 0.322 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs6501455; hg19: chr17-69201811;