rs17645907

Variant names:

• chr7-76659716-T-C
• rs17645907

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 0.261 in 151,934 control chromosomes in the GnomAD database, including 5,234 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 0.26 (5234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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: 0.261 AC: 39670 AN: 151818 Hom.: 5229 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0167

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.261 AC: 39706 AN: 151934 Hom.: 5234 Cov.: 32 AF XY: 0.260 AC XY: 19330 AN XY: 74280

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.270

Alfa AF: 0.266 Hom.: 6590

Bravo AF: 0.262

Asia WGS AF: 0.130 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17645907; hg19: chr7-76289033;