rs963193

Variant names:

• chr6-151468220-T-A
• rs963193
• NM_024573.3:c.559-123T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-151468220-T-A
• chr6-151468220-T-G

Variant summary

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

The NM_024573.3(DCPH1):​c.559-123T>A 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DCPH1 NM_024573.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 11 publications found

Genes affected

DCPH1 (HGNC:17872): (acidic residue methyltransferase 1) Enables S-adenosylmethionine-dependent methyltransferase activity; enzyme binding activity; and protein carboxyl O-methyltransferase activity. Involved in methylation and regulation of response to DNA damage stimulus. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCPH1	NM_024573.3	c.559-123T>A		intron_variant	Intron 4 of 4	ENST00000367294.4	NP_078849.1
DCPH1	NM_001286562.2	c.202-123T>A		intron_variant	Intron 3 of 3		NP_001273491.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMT1	ENST00000367294.4	c.559-123T>A		intron_variant	Intron 4 of 4	1	NM_024573.3	ENSP00000356263.3
ARMT1	ENST00000545879.5	c.202-123T>A		intron_variant	Intron 3 of 3	2		ENSP00000444121.1
ARMT1	ENST00000494826.1	n.*282-123T>A		intron_variant	Intron 3 of 3	2		ENSP00000435882.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 469612 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 247422

African (AFR) AF: 0.00 AC: 0 AN: 12824

American (AMR) AF: 0.00 AC: 0 AN: 16778

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13760

East Asian (EAS) AF: 0.00 AC: 0 AN: 31574

South Asian (SAS) AF: 0.00 AC: 0 AN: 39648

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33020

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1984

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 293584

Other (OTH) AF: 0.00 AC: 0 AN: 26440

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		0.080

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: rs963193; hg19: chr6-151789355;