rs434157

Variant names:

• chr5-112855945-G-A
• rs434157
• ENST00000520401.1:n.229-704G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-112855945-G-A
• chr5-112855945-G-T

Variant summary

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

The ENST00000520401.1(ENSG00000258864):​n.229-704G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 152,116 control chromosomes in the GnomAD database, including 44,004 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 0.75 (44004 hom., cov: 31)
• Consequence: ENSG00000258864 ENST00000520401.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 7 publications found

Genes affected

ENSG00000258864 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520401.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258864	ENST00000520401.1	TSL:3	n.229-704G>A		intron	N/A	ENSP00000454861.1

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114395 AN: 151998 Hom.: 43960 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.753 AC: 114494 AN: 152116 Hom.: 44004 Cov.: 31 AF XY: 0.753 AC XY: 55970 AN XY: 74360

African (AFR) AF: 0.910 AC: 37812 AN: 41548

American (AMR) AF: 0.742 AC: 11343 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2151 AN: 3472

East Asian (EAS) AF: 0.902 AC: 4673 AN: 5180

South Asian (SAS) AF: 0.762 AC: 3666 AN: 4810

European-Finnish (FIN) AF: 0.631 AC: 6650 AN: 10534

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45820 AN: 67972

Other (OTH) AF: 0.738 AC: 1554 AN: 2106

Alfa AF: 0.738 Hom.: 15542

Bravo AF: 0.770

Asia WGS AF: 0.812 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs434157; hg19: chr5-112191642;