rs535043

Variant names:

• chr1-238532736-G-A
• rs535043
• ENST00000442726.1:n.217-713G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-238532736-G-A
• chr1-238532736-G-C

Variant summary

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

The ENST00000442726.1(ENSG00000231877):​n.217-713G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,946 control chromosomes in the GnomAD database, including 35,844 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 0.68 (35844 hom., cov: 32)
• Consequence: ENSG00000231877 ENST00000442726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

Genes affected

ENSG00000231877 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.744 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
ENSG00000231877	ENST00000442726.1	n.217-713G>A		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103896 AN: 151828 Hom.: 35818 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.684 AC: 103978 AN: 151946 Hom.: 35844 Cov.: 32 AF XY: 0.681 AC XY: 50578 AN XY: 74276

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.700

Alfa AF: 0.706 Hom.: 60414

Bravo AF: 0.689

Asia WGS AF: 0.593 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs535043; hg19: chr1-238696036;