10-68114347-CTTTTT-CTTTT

Variant names:

• chr10-68114347-CT-C
• rs200370503
• NM_032578.4:c.-2+4638delT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_032578.4(MYPN):​c.-2+4638delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: MYPN NM_032578.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627

Genes affected

MYPN (HGNC:23246): (myopalladin) Striated muscle in vertebrates comprises large proteins which must be organized properly to contract efficiently. Z-lines in striated muscle are a sign of this organization, representing the ends of actin thin filaments, titin, nebulin or nebulette and accessory proteins required for structure and function. This gene encodes a protein which interacts with nebulin in skeletal muscle or nebulette in cardiac muscle and alpha-actinin. In addition, this gene product can interact with a protein with the I-band indicating it has a regulatory as well as structural function. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00145 (196/135466) while in subpopulation NFE AF= 0.00173 (110/63692). AF 95% confidence interval is 0.00146. There are 0 homozygotes in gnomad4. There are 109 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 196 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYPN	NM_032578.4	c.-2+4638delT		intron_variant	Intron 1 of 19	ENST00000358913.10	NP_115967.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYPN	ENST00000358913.10	c.-2+4625delT		intron_variant	Intron 1 of 19	1	NM_032578.4	ENSP00000351790.5

Frequencies

GnomAD3 genomes AF: 0.00145 AC: 196 AN: 135466 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000521

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000980

Gnomad ASJ AF: 0.00120

Gnomad EAS AF: 0.000212

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00612

Gnomad MID AF: 0.00360

Gnomad NFE AF: 0.00173

Gnomad OTH AF: 0.00382

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

GnomAD4 genome AF: 0.00145 AC: 196 AN: 135466 Hom.: 0 Cov.: 0 AF XY: 0.00168 AC XY: 109 AN XY: 64864

Gnomad4 AFR AF: 0.000520

Gnomad4 AMR AF: 0.000979

Gnomad4 ASJ AF: 0.00120

Gnomad4 EAS AF: 0.000212

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00612

Gnomad4 NFE AF: 0.00173

Gnomad4 OTH AF: 0.00380

Alfa AF: 0.000297 Hom.: 138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs200370503; hg19: chr10-69874104;