14-39023441-T-C

Position:

• chr14-39023441-T-C

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 0.75 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.750 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

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.745

Alfa AF: 0.780 Hom.: 24636

Bravo AF: 0.742

Asia WGS AF: 0.713 AC: 2482 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
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: rs2038358; hg19: chr14-39492645;