rs560787592

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001110199.3(SRRM3):​c.748C>A​(p.Arg250Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000552 in 1,449,526 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 30)
Exomes 𝑓: 0.0000055 ( 0 hom. )

Consequence

SRRM3
NM_001110199.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.925
Variant links:
Genes affected
SRRM3 (HGNC:26729): (serine/arginine repetitive matrix 3) Predicted to enable mRNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 8 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SRRM3NM_001110199.3 linkc.748C>A p.Arg250Arg synonymous_variant Exon 10 of 15 ENST00000611745.2 NP_001103669.1 A0A087WXA3
SRRM3NM_001291831.2 linkc.748C>A p.Arg250Arg synonymous_variant Exon 10 of 16 NP_001278760.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SRRM3ENST00000611745.2 linkc.748C>A p.Arg250Arg synonymous_variant Exon 10 of 15 5 NM_001110199.3 ENSP00000480851.1 A0A087WXA3
SRRM3ENST00000464752.1 linkc.-21C>A upstream_gene_variant 2 ENSP00000483698.1 A0A087X0W5

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.00000552
AC:
8
AN:
1449526
Hom.:
0
Cov.:
30
AF XY:
0.00000832
AC XY:
6
AN XY:
720772
show subpopulations
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:
0.00000723
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
12
DANN
Benign
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.21
Details are displayed if max score is > 0.2
DS_AL_spliceai
0.21
Position offset: -22

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: chr7-75894704; API