14-27006274-T-C

Position:

• chr14-27006274-T-C

Variant summary

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

The ENST00000656336.1(ENSG00000258081):​n.481-127696T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,000 control chromosomes in the GnomAD database, including 15,523 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 0.43 (15523 hom., cov: 32)
• Consequence: ENST00000656336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656336.1	n.481-127696T>C		intron_variant, non_coding_transcript_variant
	ENST00000552303.1	n.206-70964T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65005 AN: 151884 Hom.: 15519 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.428 AC: 65022 AN: 152000 Hom.: 15523 Cov.: 32 AF XY: 0.429 AC XY: 31835 AN XY: 74288

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.462

Alfa AF: 0.527 Hom.: 28122

Bravo AF: 0.420

Asia WGS AF: 0.372 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.35
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8020291; hg19: chr14-27475480;