14-26937686-G-T

Position:

• chr14-26937686-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The variant allele was found at a frequency of 0.021 in 151,804 control chromosomes in the GnomAD database, including 52 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 0.021 (52 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.021 (3181/151804) while in subpopulation AFR AF= 0.0496 (2056/41456). AF 95% confidence interval is 0.0478. There are 52 homozygotes in gnomad4. There are 1474 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 52 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26937686G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258081	ENST00000552303.1	n.205+94030G>T		intron_variant		4
ENSG00000258081	ENST00000656336.1	n.481-196284G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0209 AC: 3173 AN: 151686 Hom.: 52 Cov.: 32

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0234

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00997

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0210 AC: 3181 AN: 151804 Hom.: 52 Cov.: 32 AF XY: 0.0199 AC XY: 1474 AN XY: 74188

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.0139

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.0236

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00997

Gnomad4 OTH AF: 0.0228

Alfa AF: 0.0100 Hom.: 8

Bravo AF: 0.0224

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17111920; hg19: chr14-27406892;