rs3917878

Variant names:

• chr17-34251836-C-T
• rs3917878

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 0.0996 in 152,236 control chromosomes in the GnomAD database, including 889 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 0.10 (889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 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: 0.0995 AC: 15136 AN: 152118 Hom.: 885 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0996 AC: 15156 AN: 152236 Hom.: 889 Cov.: 32 AF XY: 0.0981 AC XY: 7305 AN XY: 74430

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0738

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0669

Gnomad4 NFE AF: 0.0824

Gnomad4 OTH AF: 0.106

Alfa AF: 0.101 Hom.: 81

Bravo AF: 0.102

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3917878; hg19: chr17-32578855;