rs3138052

Variant names:

• chr14-35405815-T-C
• rs3138052

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 152,022 control chromosomes in the GnomAD database, including 5,349 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 (5349 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 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: 39638 AN: 151904 Hom.: 5346 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.261 AC: 39661 AN: 152022 Hom.: 5349 Cov.: 32 AF XY: 0.255 AC XY: 18960 AN XY: 74304

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.241

Alfa AF: 0.261 Hom.: 785

Bravo AF: 0.258

Asia WGS AF: 0.186 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3138052; hg19: chr14-35875021;