14-60240713-C-T

Position:

• chr14-60240713-C-T

Variant summary

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

The ENST00000532515.1(ENSG00000254718):​n.2267G>A 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 0.346 in 152,054 control chromosomes in the GnomAD database, including 9,878 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 0.35 (9878 hom., cov: 33)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: ENSG00000254718 ENST00000532515.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440

Genes affected

ENSG00000254718 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927702	NR_188027.1	n.201-259G>A		intron_variant
LOC101927702	NR_188028.1	n.280-259G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254718	ENST00000532515.1	n.2267G>A		non_coding_transcript_exon_variant	2/2	1
ENSG00000254718	ENST00000529171.5	n.235-259G>A		intron_variant		3
ENSG00000254718	ENST00000553269.5	n.278-259G>A		intron_variant		3
ENSG00000254718	ENST00000553775.1	n.133-259G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52486 AN: 151924 Hom.: 9861 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.325

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.346 AC: 52544 AN: 152044 Hom.: 9878 Cov.: 33 AF XY: 0.341 AC XY: 25326 AN XY: 74306

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.321

Alfa AF: 0.309 Hom.: 1374

Bravo AF: 0.350

Asia WGS AF: 0.275 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11628587; hg19: chr14-60707431;