14-42702125-T-C

Position:

• chr14-42702125-T-C

Variant summary

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

The ENST00000557251.1(ENSG00000258394):​n.167-980T>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 0.752 in 152,002 control chromosomes in the GnomAD database, including 43,693 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 (43693 hom., cov: 31)
• Consequence: ENST00000557251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 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
	ENST00000557251.1	n.167-980T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114201 AN: 151884 Hom.: 43655 Cov.: 31

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.752 AC: 114296 AN: 152002 Hom.: 43693 Cov.: 31 AF XY: 0.753 AC XY: 55913 AN XY: 74272

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.774

Alfa AF: 0.801 Hom.: 59822

Bravo AF: 0.743

Asia WGS AF: 0.684 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1627411; hg19: chr14-43171328;