rs796858947

Variant names:

• chr5-139307139-GTTTTT-G
• rs796858947
• NM_018834.6:c.-177-94_-177-90delTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr5-139307139-GTTTTT-G
• chr5-139307139-GTTTTT-GT
• chr5-139307139-GTTTTT-GTT
• chr5-139307139-GTTTTT-GTTT
• chr5-139307139-GTTTTT-GTTTT
• chr5-139307139-GTTTTT-GTTTTTT
• chr5-139307139-GTTTTT-GTTTTTTT

Variant summary

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

The NM_018834.6(MATR3):​c.-177-94_-177-90delTTTTT variant causes a intron change. The variant allele was found at a frequency of 0.00000679 in 147,288 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: 𝑓 0.0000068 (0 hom., cov: 32)
• Consequence: MATR3 NM_018834.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.09

Genes affected

MATR3 (HGNC:6912): (matrin 3) This gene encodes a nuclear matrix protein, which is proposed to stabilize certain messenger RNA species. Mutations of this gene are associated with distal myopathy 2, which often includes vocal cord and pharyngeal weakness. Alternatively spliced transcript variants, including read-through transcripts composed of the upstream small nucleolar RNA host gene 4 (non-protein coding) and matrin 3 gene sequence, have been identified. Pseudogenes of this gene are located on chromosomes 1 and X. [provided by RefSeq, Aug 2013]

MATR3 (HGNC:):

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
MATR3	NM_018834.6	c.-177-94_-177-90delTTTTT		intron_variant	Intron 1 of 14	ENST00000394805.8	NP_061322.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MATR3	ENST00000394805.8	c.-177-99_-177-95delTTTTT		intron_variant	Intron 1 of 14	1	NM_018834.6	ENSP00000378284.3
MATR3	ENST00000394800.6	c.-177-99_-177-95delTTTTT		intron_variant	Intron 5 of 18	5		ENSP00000378279.2
MATR3	ENST00000502929.5	c.-177-99_-177-95delTTTTT		intron_variant	Intron 6 of 19	2		ENSP00000422319.1

Frequencies

GnomAD3 genomes AF: 0.00000679 AC: 1 AN: 147288 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000249

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000679 AC: 1 AN: 147288 Hom.: 0 Cov.: 32 AF XY: 0.0000140 AC XY: 1 AN XY: 71670

Gnomad4 AFR AF: 0.0000249

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs796858947; hg19: chr5-138642828;