rs179907

Variant names:

• chr17-69911872-T-A
• rs179907

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 0.308 in 151,934 control chromosomes in the GnomAD database, including 7,360 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 0.31 (7360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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: 0.308 AC: 46788 AN: 151816 Hom.: 7352 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.308 AC: 46822 AN: 151934 Hom.: 7360 Cov.: 32 AF XY: 0.303 AC XY: 22502 AN XY: 74240

African (AFR) AF: 0.320 AC: 13274 AN: 41428

American (AMR) AF: 0.272 AC: 4151 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1039 AN: 3472

East Asian (EAS) AF: 0.0402 AC: 208 AN: 5172

South Asian (SAS) AF: 0.205 AC: 985 AN: 4810

European-Finnish (FIN) AF: 0.306 AC: 3224 AN: 10530

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23027 AN: 67950

Other (OTH) AF: 0.301 AC: 636 AN: 2110

Alfa AF: 0.330 Hom.: 1039

Bravo AF: 0.304

Asia WGS AF: 0.132 AC: 458 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.064
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs179907; hg19: chr17-67908013;