rs17151904

Positions:

• chr7-25568789-G-A
• chr7-25568789-G-C

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 0.24 in 152,188 control chromosomes in the GnomAD database, including 4,788 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 (4788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.240 AC: 36444 AN: 152070 Hom.: 4783 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.240 AC: 36497 AN: 152188 Hom.: 4788 Cov.: 32 AF XY: 0.239 AC XY: 17773 AN XY: 74404

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.228

Alfa AF: 0.198 Hom.: 2213

Bravo AF: 0.244

Asia WGS AF: 0.369 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17151904; hg19: chr7-25608409;