rs3757316

Variant names:

• chr6-151453204-G-A
• rs3757316
• NM_024573.3:c.41+618G>A

Variant summary

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

The NM_024573.3(DCPH1):​c.41+618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,088 control chromosomes in the GnomAD database, including 17,265 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 0.46 (17265 hom., cov: 33)
• Consequence: DCPH1 NM_024573.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 13 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCPH1	NM_024573.3	c.41+618G>A		intron_variant	Intron 1 of 4	ENST00000367294.4	NP_078849.1
DCPH1	NM_001286562.2	c.-211+618G>A		intron_variant	Intron 1 of 3		NP_001273491.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMT1	ENST00000367294.4	c.41+618G>A		intron_variant	Intron 1 of 4	1	NM_024573.3	ENSP00000356263.3
ARMT1	ENST00000545879.5	c.-211+618G>A		intron_variant	Intron 1 of 3	2		ENSP00000444121.1
ARMT1	ENST00000483931.1	n.277+404G>A		intron_variant	Intron 1 of 3	3
ARMT1	ENST00000494826.1	n.41+618G>A		intron_variant	Intron 1 of 3	2		ENSP00000435882.1

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69200 AN: 151970 Hom.: 17239 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.455 AC: 69274 AN: 152088 Hom.: 17265 Cov.: 33 AF XY: 0.457 AC XY: 33953 AN XY: 74328

African (AFR) AF: 0.666 AC: 27633 AN: 41490

American (AMR) AF: 0.421 AC: 6436 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1465 AN: 3472

East Asian (EAS) AF: 0.602 AC: 3108 AN: 5164

South Asian (SAS) AF: 0.458 AC: 2206 AN: 4818

European-Finnish (FIN) AF: 0.318 AC: 3362 AN: 10562

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23712 AN: 67970

Other (OTH) AF: 0.446 AC: 942 AN: 2112

Alfa AF: 0.374 Hom.: 13973

Bravo AF: 0.473

Asia WGS AF: 0.540 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.57
PhyloP100		0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3757316; hg19: chr6-151774339;