rs179907

Variant names:

• chr17-69911872-T-A
• rs179907

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 0.308 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.308 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

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.0402

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.301

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs179907; hg19: chr17-67908013;