14-39023441-T-C

Variant names:

• chr14-39023441-T-C
• rs2038358

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 0.75 in 151,990 control chromosomes in the GnomAD database, including 43,100 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 0.75 (43100 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113978 AN: 151872 Hom.: 43086 Cov.: 30

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.750 AC: 114040 AN: 151990 Hom.: 43100 Cov.: 30 AF XY: 0.746 AC XY: 55420 AN XY: 74276

African (AFR) AF: 0.697 AC: 28906 AN: 41458

American (AMR) AF: 0.679 AC: 10367 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2667 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4114 AN: 5176

South Asian (SAS) AF: 0.698 AC: 3355 AN: 4806

European-Finnish (FIN) AF: 0.773 AC: 8148 AN: 10540

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.795 AC: 54027 AN: 67966

Other (OTH) AF: 0.745 AC: 1569 AN: 2106

Alfa AF: 0.780 Hom.: 27005

Bravo AF: 0.742

Asia WGS AF: 0.713 AC: 2482 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.52
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs2038358; hg19: chr14-39492645;