rs179913

Variant names:

• chr17-69907502-G-A
• rs179913

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 0.24 in 152,128 control chromosomes in the GnomAD database, including 5,327 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 0.24 (5327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 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: 0.240 AC: 36440 AN: 152010 Hom.: 5327 Cov.: 32

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.240 AC: 36445 AN: 152128 Hom.: 5327 Cov.: 32 AF XY: 0.236 AC XY: 17585 AN XY: 74356

African (AFR) AF: 0.0866 AC: 3594 AN: 41524

American (AMR) AF: 0.245 AC: 3748 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3466

East Asian (EAS) AF: 0.0404 AC: 209 AN: 5170

South Asian (SAS) AF: 0.194 AC: 936 AN: 4826

European-Finnish (FIN) AF: 0.306 AC: 3230 AN: 10566

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22900 AN: 67984

Other (OTH) AF: 0.251 AC: 529 AN: 2106

Alfa AF: 0.302 Hom.: 10513

Bravo AF: 0.225

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.46
DANN	Benign	0.66
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs179913; hg19: chr17-67903643;