rs1029482

Variant names:

• chr7-43215011-C-A
• rs1029482
• NM_015052.5:c.-31-28864C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-43215011-C-A
• chr7-43215011-C-G
• chr7-43215011-C-T

Variant summary

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

The NM_015052.5(HECW1):​c.-31-28864C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,160 control chromosomes in the GnomAD database, including 38,438 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 0.71 (38438 hom., cov: 33)
• Consequence: HECW1 NM_015052.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 5 publications found

Genes affected

HECW1 (HGNC:22195): (HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including cellular protein metabolic process; negative regulation of sodium ion transmembrane transporter activity; and regulation of dendrite morphogenesis. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015052.5. 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
	HECW1	NM_015052.5	MANE Select	c.-31-28864C>A		intron	N/A	NP_055867.3
	HECW1	NM_001287059.2		c.-31-28864C>A		intron	N/A	NP_001273988.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HECW1	ENST00000395891.7	TSL:1 MANE Select	c.-31-28864C>A		intron	N/A	ENSP00000379228.1
	HECW1	ENST00000453890.5	TSL:2	c.-31-28864C>A		intron	N/A	ENSP00000407774.1
	HECW1	ENST00000490954.2	TSL:4	n.310-96752C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107757 AN: 152042 Hom.: 38396 Cov.: 33

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.709 AC: 107853 AN: 152160 Hom.: 38438 Cov.: 33 AF XY: 0.710 AC XY: 52848 AN XY: 74388

African (AFR) AF: 0.760 AC: 31547 AN: 41494

American (AMR) AF: 0.749 AC: 11458 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2075 AN: 3470

East Asian (EAS) AF: 0.891 AC: 4619 AN: 5186

South Asian (SAS) AF: 0.637 AC: 3074 AN: 4826

European-Finnish (FIN) AF: 0.682 AC: 7214 AN: 10574

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.672 AC: 45668 AN: 67996

Other (OTH) AF: 0.687 AC: 1452 AN: 2114

Alfa AF: 0.675 Hom.: 63079

Bravo AF: 0.717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.28
PhyloP100		-0.071
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs1029482; hg19: chr7-43254610;