14-42702125-T-C

Variant names:

• chr14-42702125-T-C
• rs1627411
• ENST00000557251.1:n.167-980T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557251.1(ENSG00000258394):​n.167-980T>C variant causes a intron 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: ENSG00000258394 ENST00000557251.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 2 publications found

Genes affected

ENSG00000258394 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557251.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258394	ENST00000557251.1	TSL:5	n.167-980T>C		intron	N/A

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

African (AFR) AF: 0.624 AC: 25862 AN: 41424

American (AMR) AF: 0.808 AC: 12334 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2705 AN: 3468

East Asian (EAS) AF: 0.555 AC: 2859 AN: 5152

South Asian (SAS) AF: 0.709 AC: 3425 AN: 4828

European-Finnish (FIN) AF: 0.847 AC: 8955 AN: 10568

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55572 AN: 67972

Other (OTH) AF: 0.774 AC: 1637 AN: 2114

Alfa AF: 0.796 Hom.: 73561

Bravo AF: 0.743

Asia WGS AF: 0.684 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.83
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs1627411; hg19: chr14-43171328;