rs1627270

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.758 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258394	ENST00000557251.1	TSL:5	n.167-3583T>A		intron	N/A

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

African (AFR) AF: 0.584 AC: 24220 AN: 41448

American (AMR) AF: 0.716 AC: 10935 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2313 AN: 3470

East Asian (EAS) AF: 0.551 AC: 2843 AN: 5162

South Asian (SAS) AF: 0.640 AC: 3088 AN: 4828

European-Finnish (FIN) AF: 0.806 AC: 8480 AN: 10526

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.764 AC: 51896 AN: 67956

Other (OTH) AF: 0.723 AC: 1526 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		0.0070

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1627270;

hg19: chr14-43168725;