rs3138056

chr14-35399308-C-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 0.344 in 151,998 control chromosomes in the GnomAD database, including 9,233 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 0.34 (9233 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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 (AMR) allele frequency at 95% confidence interval = 0.463 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: 0.344 AC: 52201 AN: 151882 Hom.: 9219 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.344 AC: 52258 AN: 151998 Hom.: 9233 Cov.: 31 AF XY: 0.347 AC XY: 25810 AN XY: 74296

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.331

Alfa AF: 0.327 Hom.: 11279

Bravo AF: 0.355

Asia WGS AF: 0.402 AC: 1401 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	0.23
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3138056; hg19: chr14-35868514;