SRRM3 p.Arg250Arg

Variant names:

• chr7-76265385-C-C
• NM_001110199.3:c.

Your query was ambiguous. Multiple possible variants found:

• chr7-76265386--
• chr7-76265388-G-T
• chr7-76265388-G-C
• chr7-76265388-G-A
• chr7-76265386-C-A
• chr7-76265386-CGG-AGA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001110199.3(SRRM3):​c. variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: SRRM3 NM_001110199.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.925
• Publications: 0 publications found

Genes affected

SRRM3 (HGNC:26729): (serine/arginine repetitive matrix 3) Predicted to enable mRNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001110199.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRRM3	NM_001110199.3	MANE Select	c.		splice_region intron	N/A	NP_001103669.1	A0A087WXA3
	SRRM3	NM_001291831.2		c.		splice_region intron	N/A	NP_001278760.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRRM3	ENST00000611745.2	TSL:5 MANE Select	c.		splice_donor intron	N/A	ENSP00000480851.1	A0A087WXA3
	SRRM3	ENST00000464752.1	TSL:2	c.		splice_donor intron	N/A	ENSP00000483698.1	A0A087X0W5
	SRRM3	ENST00000464752.1	TSL:2	c.		upstream_gene	N/A	ENSP00000483698.1	A0A087X0W5

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.93

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr7-75894703;