14-42693894-A-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000258394 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258394	ENST00000557251.1	n.167-9211A>T		intron_variant	Intron 2 of 3	5

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

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.719

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1712738; hg19: chr14-43163097;