rs3138045

chr14-35408515-T-Cchr14-35408515-T-G

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 0.213 in 152,214 control chromosomes in the GnomAD database, including 3,531 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 0.21 (3531 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32328 AN: 152096 Hom.: 3528 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.213 AC: 32354 AN: 152214 Hom.: 3531 Cov.: 33 AF XY: 0.209 AC XY: 15570 AN XY: 74422

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.193

Alfa AF: 0.209 Hom.: 6488

Bravo AF: 0.213

Asia WGS AF: 0.156 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.11
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3138045; hg19: chr14-35877721;