rs17172526

Positions:

• chr7-35944418-G-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 0.169 in 152,020 control chromosomes in the GnomAD database, including 3,649 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 0.17 (3649 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25735 AN: 151906 Hom.: 3647 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0933

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.169 AC: 25767 AN: 152020 Hom.: 3649 Cov.: 31 AF XY: 0.164 AC XY: 12174 AN XY: 74336

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.0962

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0416

Gnomad4 FIN AF: 0.0553

Gnomad4 NFE AF: 0.0933

Gnomad4 OTH AF: 0.157

Alfa AF: 0.108 Hom.: 1367

Bravo AF: 0.183

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17172526; hg19: chr7-35984028;