rs3138035

Variant names:

• chr17-34318930-C-T
• rs3138035

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 0.274 in 152,358 control chromosomes in the GnomAD database, including 6,739 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 0.27 (6726 hom., cov: 33)
  • Exomes 𝑓: 0.38 (13 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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: 0.274 AC: 41600 AN: 152022 Hom.: 6726 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.375 AC: 81 AN: 216 Hom.: 13 AF XY: 0.331 AC XY: 39 AN XY: 118

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.355

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.405

GnomAD4 genome AF: 0.273 AC: 41596 AN: 152142 Hom.: 6726 Cov.: 33 AF XY: 0.274 AC XY: 20383 AN XY: 74358

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.0954

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.270

Alfa AF: 0.337 Hom.: 12110

Bravo AF: 0.249

Asia WGS AF: 0.151 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.057
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3138035; hg19: chr17-32645949;