14-42693894-A-T

Variant names:

• chr14-42693894-A-T
• rs1712738
• ENST00000557251.1:n.167-9211A>T

Variant summary

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

The ENST00000557251.1(ENSG00000258394):​n.167-9211A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,004 control chromosomes in the GnomAD database, including 37,712 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 0.70 (37712 hom., cov: 32)
• Consequence: ENSG00000258394 ENST00000557251.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.641
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 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.167-9211A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105984 AN: 151886 Hom.: 37687 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.698 AC: 106063 AN: 152004 Hom.: 37712 Cov.: 32 AF XY: 0.699 AC XY: 51913 AN XY: 74300

African (AFR) AF: 0.571 AC: 23670 AN: 41422

American (AMR) AF: 0.718 AC: 10953 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2355 AN: 3466

East Asian (EAS) AF: 0.553 AC: 2857 AN: 5164

South Asian (SAS) AF: 0.648 AC: 3121 AN: 4818

European-Finnish (FIN) AF: 0.806 AC: 8523 AN: 10572

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52146 AN: 67980

Other (OTH) AF: 0.719 AC: 1521 AN: 2114

Alfa AF: 0.739 Hom.: 5253

Bravo AF: 0.683

Asia WGS AF: 0.647 AC: 2253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.67
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs1712738; hg19: chr14-43163097;