rs1627270

Variant names:

• chr14-42699522-T-A
• rs1627270
• ENST00000557251.1:n.167-3583T>A

Variant summary

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

The ENST00000557251.1(ENSG00000258394):​n.167-3583T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,986 control chromosomes in the GnomAD database, including 37,756 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 (37756 hom., cov: 33)
• Consequence: ENSG00000258394 ENST00000557251.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

ENSG00000258394 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.758 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.167-3583T>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106133 AN: 151868 Hom.: 37726 Cov.: 33

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.699 AC: 106217 AN: 151986 Hom.: 37756 Cov.: 33 AF XY: 0.699 AC XY: 51941 AN XY: 74312

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.723

Alfa AF: 0.739 Hom.: 5244

Bravo AF: 0.684

Asia WGS AF: 0.642 AC: 2213 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1627270; hg19: chr14-43168725;