rs12645412

Variant names:

• chr4-83431597-T-A
• rs12645412
• NM_133636.5:c.2295+67A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-83431597-T-A
• chr4-83431597-T-C
• chr4-83431597-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_133636.5(HELQ):​c.2295+67A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HELQ NM_133636.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 5 publications found

Genes affected

HELQ (HGNC:18536): (helicase, POLQ like) HEL308 is a single-stranded DNA-dependent ATPase and DNA helicase (Marini and Wood, 2002 [PubMed 11751861]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HELQ	NM_133636.5	c.2295+67A>T		intron_variant	Intron 11 of 17	ENST00000295488.8	NP_598375.3
HELQ	NM_001297755.2	c.2094+67A>T		intron_variant	Intron 10 of 16		NP_001284684.2
HELQ	NM_001297756.2	c.804+67A>T		intron_variant	Intron 11 of 17		NP_001284685.1
HELQ	NM_001297757.2	c.663+67A>T		intron_variant	Intron 10 of 16		NP_001284686.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HELQ	ENST00000295488.8	c.2295+67A>T		intron_variant	Intron 11 of 17	1	NM_133636.5	ENSP00000295488.3
HELQ	ENST00000510985.1	c.2094+67A>T		intron_variant	Intron 10 of 16	1		ENSP00000424539.1
HELQ	ENST00000508591.5	n.*727+67A>T		intron_variant	Intron 10 of 16	1		ENSP00000424186.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 484208 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 262502

African (AFR) AF: 0.00 AC: 0 AN: 10320

American (AMR) AF: 0.00 AC: 0 AN: 20170

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14328

East Asian (EAS) AF: 0.00 AC: 0 AN: 26184

South Asian (SAS) AF: 0.00 AC: 0 AN: 29944

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2176

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 314902

Other (OTH) AF: 0.00 AC: 0 AN: 24556

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1521

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.11
PhyloP100		1.2

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: rs12645412; hg19: chr4-84352750;