rs560787592

Variant names:

• chr7-76265386-C-A
• NM_001110199.3:c.748C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-76265386-C-A
• chr7-76265386-C-G
• chr7-76265386-C-T

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.925

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

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
SRRM3	NM_001110199.3	c.748C>A	p.Arg250Arg	synonymous_variant	Exon 10 of 15	ENST00000611745.2	NP_001103669.1
SRRM3	NM_001291831.2	c.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
SRRM3	ENST00000611745.2	c.748C>A	p.Arg250Arg	synonymous_variant	Exon 10 of 15	5	NM_001110199.3	ENSP00000480851.1
SRRM3	ENST00000464752.1	c.-21C>A		upstream_gene_variant		2		ENSP00000483698.1

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

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;