rs3138056

Variant names:

• chr14-35399308-C-T
• rs3138056

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.345 AC: 14289 AN: 41446

American (AMR) AF: 0.472 AC: 7219 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3466

East Asian (EAS) AF: 0.356 AC: 1836 AN: 5158

South Asian (SAS) AF: 0.403 AC: 1944 AN: 4820

European-Finnish (FIN) AF: 0.314 AC: 3310 AN: 10542

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21422 AN: 67970

Other (OTH) AF: 0.331 AC: 699 AN: 2112

Alfa AF: 0.329 Hom.: 15171

Bravo AF: 0.355

Asia WGS AF: 0.402 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.23
DANN	Benign	0.52
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3138056; hg19: chr14-35868514;