rs179907

Positions:

• chr17-69911872-T-A

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.69911872T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;