rs17706620

Variant names:

• chr7-41878941-T-C
• rs17706620

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 0.313 in 152,154 control chromosomes in the GnomAD database, including 8,862 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 (8862 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 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: 0.314 AC: 47667 AN: 152036 Hom.: 8855 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.313 AC: 47687 AN: 152154 Hom.: 8862 Cov.: 32 AF XY: 0.315 AC XY: 23450 AN XY: 74354

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.332

Alfa AF: 0.363 Hom.: 2707

Bravo AF: 0.283

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17706620; hg19: chr7-41918539;