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. Variant got -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

Genes affected

ENSG00000258864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000258864	ENST00000520401.1	n.229-704G>A		intron_variant	Intron 3 of 7	3		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

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.738

Alfa AF: 0.742 Hom.: 8857

Bravo AF: 0.770

Asia WGS AF: 0.812 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs434157; hg19: chr5-112191642;