rs4659762

Variant names:

• chr1-237003918-A-C
• rs4659762
• ENST00000785372.1:n.827+1825A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-237003918-A-C
• chr1-237003918-A-G

Variant summary

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

The ENST00000785372.1(ENSG00000302268):​n.827+1825A>C 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: 33)
• Consequence: ENSG00000302268 ENST00000785372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 0 publications found

Genes affected

ENSG00000302268 (HGNC:):

MT1HL1 (HGNC:31864): (metallothionein 1H like 1) This gene is a retrotransposed gene, compared to MT1H (GeneID:4496). This retrogene is transcribed. It retains a full-length CDS, and is assumed to be translated. Compared to the MT1H product, this protein product differs at three internal amino acids, two of which are at metal-binding sites. [provided by RefSeq, Mar 2013]

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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MT1HL1	NM_001276687.2	c.*269T>G		downstream_gene_variant		ENST00000464121.3	NP_001263616.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT1HL1	ENST00000464121.3	c.*269T>G		downstream_gene_variant		6	NM_001276687.2	ENSP00000476141.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.53
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs4659762; hg19: chr1-237167218;