17-70310696-G-A

Variant names:

• chr17-70310696-G-A
• rs312729

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 0.45 in 151,974 control chromosomes in the GnomAD database, including 15,455 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 0.45 (15455 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68340 AN: 151856 Hom.: 15436 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.450 AC: 68390 AN: 151974 Hom.: 15455 Cov.: 32 AF XY: 0.447 AC XY: 33219 AN XY: 74296

African (AFR) AF: 0.446 AC: 18494 AN: 41428

American (AMR) AF: 0.449 AC: 6846 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2479 AN: 5164

South Asian (SAS) AF: 0.468 AC: 2259 AN: 4828

European-Finnish (FIN) AF: 0.377 AC: 3978 AN: 10554

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31225 AN: 67952

Other (OTH) AF: 0.435 AC: 919 AN: 2114

Alfa AF: 0.458 Hom.: 58706

Bravo AF: 0.456

Asia WGS AF: 0.467 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.69
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs312729; hg19: chr17-68306837;