14-102771441-G-A

Position:

• chr14-102771441-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000559402.1(ENSG00000259508):​n.258C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,202 control chromosomes in the GnomAD database, including 19,473 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 0.47 (19471 hom., cov: 32)
  • Exomes 𝑓: 0.21 (2 hom.)
• Consequence: ENSG00000259508 ENST00000559402.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

ENSG00000259508 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102771441G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259508	ENST00000559402.1	n.258C>T		non_coding_transcript_exon_variant	2/2	4
ENSG00000259508	ENST00000559675.1	n.152-986C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71141 AN: 151946 Hom.: 19433 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.435

GnomAD4 exome AF: 0.210 AC: 29 AN: 138 Hom.: 2 Cov.: 0 AF XY: 0.179 AC XY: 20 AN XY: 112

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.469 AC: 71246 AN: 152064 Hom.: 19471 Cov.: 32 AF XY: 0.468 AC XY: 34761 AN XY: 74328

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.435

Alfa AF: 0.367 Hom.: 9775

Bravo AF: 0.491

Asia WGS AF: 0.475 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.022
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7143468; hg19: chr14-103237778;