14-31884044-T-C

Variant names:

• chr14-31884044-T-C
• rs2039485

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 0.203 in 152,182 control chromosomes in the GnomAD database, including 3,719 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 0.20 (3719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 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: 0.203 AC: 30869 AN: 152066 Hom.: 3718 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.203 AC: 30892 AN: 152182 Hom.: 3719 Cov.: 32 AF XY: 0.210 AC XY: 15649 AN XY: 74392

African (AFR) AF: 0.102 AC: 4223 AN: 41542

American (AMR) AF: 0.239 AC: 3660 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3468

East Asian (EAS) AF: 0.496 AC: 2561 AN: 5166

South Asian (SAS) AF: 0.373 AC: 1799 AN: 4820

European-Finnish (FIN) AF: 0.250 AC: 2643 AN: 10592

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14860 AN: 67982

Other (OTH) AF: 0.211 AC: 445 AN: 2112

Alfa AF: 0.218 Hom.: 18412

Bravo AF: 0.197

Asia WGS AF: 0.372 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2039485; hg19: chr14-32353250;