rs17706620

Positions:

• chr7-41878941-T-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 0.313 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;