chr14-85754586-T-G

Variant names:

• chr14-85754586-T-G
• rs12879941

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 0.4 in 151,914 control chromosomes in the GnomAD database, including 13,006 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 0.40 (13006 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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: 0.401 AC: 60829 AN: 151796 Hom.: 13010 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.400 AC: 60839 AN: 151914 Hom.: 13006 Cov.: 31 AF XY: 0.399 AC XY: 29601 AN XY: 74238

African (AFR) AF: 0.265 AC: 10982 AN: 41482

American (AMR) AF: 0.395 AC: 6013 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3470

East Asian (EAS) AF: 0.163 AC: 838 AN: 5144

South Asian (SAS) AF: 0.326 AC: 1569 AN: 4818

European-Finnish (FIN) AF: 0.500 AC: 5280 AN: 10562

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33074 AN: 67920

Other (OTH) AF: 0.415 AC: 875 AN: 2106

Alfa AF: 0.438 Hom.: 2643

Bravo AF: 0.389

Asia WGS AF: 0.266 AC: 926 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.68
DANN	Benign	0.45
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs12879941; hg19: chr14-86220930;