rs3138050

Variant names:

• chr14-35406163-G-A
• rs3138050

Your query was ambiguous. Multiple possible variants found:

• chr14-35406163-G-A
• chr14-35406163-G-C
• chr14-35406163-G-T

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 0.234 in 151,542 control chromosomes in the GnomAD database, including 4,193 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 0.23 (4193 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 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: 0.234 AC: 35429 AN: 151424 Hom.: 4184 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.234 AC: 35461 AN: 151542 Hom.: 4193 Cov.: 31 AF XY: 0.234 AC XY: 17328 AN XY: 74066

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.215

Alfa AF: 0.122 Hom.: 227

Bravo AF: 0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3138050; hg19: chr14-35875369;