rs179562

Variant names:

• chr14-30755252-G-A
• rs179562
• ENST00000554665.1:n.257-20153C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-30755252-G-A
• chr14-30755252-G-C

Variant summary

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

The ENST00000554665.1(ENSG00000258558):​n.257-20153C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,008 control chromosomes in the GnomAD database, including 32,545 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 0.62 (32545 hom., cov: 31)
• Consequence: ENSG00000258558 ENST00000554665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 11 publications found

Genes affected

ENSG00000258558 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554665.1. 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
	ENSG00000258558	ENST00000554665.1	TSL:3	n.257-20153C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93884 AN: 151890 Hom.: 32549 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.618 AC: 93891 AN: 152008 Hom.: 32545 Cov.: 31 AF XY: 0.619 AC XY: 46013 AN XY: 74312

African (AFR) AF: 0.282 AC: 11682 AN: 41448

American (AMR) AF: 0.613 AC: 9361 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2366 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3189 AN: 5136

South Asian (SAS) AF: 0.742 AC: 3571 AN: 4812

European-Finnish (FIN) AF: 0.780 AC: 8247 AN: 10572

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53240 AN: 67976

Other (OTH) AF: 0.648 AC: 1367 AN: 2108

Alfa AF: 0.732 Hom.: 46996

Bravo AF: 0.587

Asia WGS AF: 0.635 AC: 2210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.77
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs179562; hg19: chr14-31224458;