chr1-238532736-G-A

Variant names:

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

Variant summary

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

The ENST00000442726.1(ENSG00000234464):​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: ENSG00000234464 ENST00000442726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 4 publications found

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442726.1. 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
	ENSG00000234464	ENST00000442726.1	TSL:2	n.217-713G>A		intron	N/A
	ENSG00000234464	ENST00000716151.1		n.547+33446G>A		intron	N/A
	ENSG00000234464	ENST00000716155.1		n.297-713G>A		intron	N/A

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

African (AFR) AF: 0.632 AC: 26176 AN: 41426

American (AMR) AF: 0.755 AC: 11525 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2343 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3173 AN: 5174

South Asian (SAS) AF: 0.565 AC: 2724 AN: 4818

European-Finnish (FIN) AF: 0.674 AC: 7091 AN: 10522

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48561 AN: 67962

Other (OTH) AF: 0.700 AC: 1476 AN: 2108

Alfa AF: 0.703 Hom.: 146949

Bravo AF: 0.689

Asia WGS AF: 0.593 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.15
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs535043; hg19: chr1-238696036;