6-7570492-A-G

Variant names:

• chr6-7570492-A-G
• NM_004415.4:c.1630A>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004415.4(DSP):​c.1630A>G​(p.Met544Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,856 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: DSP NM_004415.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.25

Genes affected

DSP (HGNC:3052): (desmoplakin) This gene encodes a protein that anchors intermediate filaments to desmosomal plaques and forms an obligate component of functional desmosomes. Mutations in this gene are the cause of several cardiomyopathies and keratodermas, including skin fragility-woolly hair syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSP	NM_004415.4	c.1630A>G	p.Met544Val	missense_variant	Exon 13 of 24	ENST00000379802.8	NP_004406.2
DSP	NM_001319034.2	c.1630A>G	p.Met544Val	missense_variant	Exon 13 of 24		NP_001305963.1
DSP	NM_001008844.3	c.1630A>G	p.Met544Val	missense_variant	Exon 13 of 24		NP_001008844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSP	ENST00000379802.8	c.1630A>G	p.Met544Val	missense_variant	Exon 13 of 24	1	NM_004415.4	ENSP00000369129.3
DSP	ENST00000418664.2	c.1630A>G	p.Met544Val	missense_variant	Exon 13 of 24	1		ENSP00000396591.2
DSP	ENST00000710359.1	c.1630A>G	p.Met544Val	missense_variant	Exon 13 of 24			ENSP00000518230.1
DSP	ENST00000684395.1	n.14A>G		non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461856 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727226

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Uncertain	0.0
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.73	D;.
Eigen	Uncertain	0.32
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.86	D;D
M_CAP	Benign	0.040	D
MetaRNN	Uncertain	0.53	D;D
MetaSVM	Benign	-0.51	T
MutationAssessor	Benign	1.6	L;L
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	-2.4	N;N
REVEL	Uncertain	0.47
Sift	Benign	0.064	T;T
Sift4G	Benign	0.29	T;T
Polyphen		0.28	B;.
Vest4		0.65
MutPred		0.35		Gain of methylation at K545 (P = 0.0394);Gain of methylation at K545 (P = 0.0394);
MVP		0.82
MPC		0.76
ClinPred		0.85	D
GERP RS		5.8
Varity_R		0.63
gMVP		0.72

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-7570725;