rs3767206

chr1-70249410-G-Achr1-70249410-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350605.2(SRSF11):c.1023-542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,280 control chromosomes in the GnomAD database, including 1,243 homozygotes. 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: 𝑓 0.12 (1243 hom., cov: 32)
  • Exomes 𝑓: 0.074 (0 hom.)
• Consequence: SRSF11 NM_001350605.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

SRSF11 (HGNC:10782): (serine and arginine rich splicing factor 11) This gene encodes 54-kD nuclear protein that contains an arginine/serine-rich region similar to segments found in pre-mRNA splicing factors. Although the function of this protein is not yet known, structure and immunolocalization data suggest that it may play a role in pre-mRNA processing. Alternative splicing results in multiple transcript variants encoding different proteins. In addition, a pseudogene of this gene has been found on chromosome 12.[provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRSF11	NM_001350605.2	c.1023-542G>A		intron_variant		ENST00000370949.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRSF11	ENST00000370949.2	c.1023-542G>A		intron_variant		1	NM_001350605.2	P4

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17805 AN: 151974 Hom.: 1225 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.123

GnomAD4 exome AF: 0.0745 AC: 14 AN: 188 Hom.: 0 Cov.: 0 AF XY: 0.0648 AC XY: 7 AN XY: 108

Gnomad4 AMR exome AF: 0.286

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0625

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.117 AC: 17867 AN: 152092 Hom.: 1243 Cov.: 32 AF XY: 0.121 AC XY: 8968 AN XY: 74336

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0722

Gnomad4 NFE AF: 0.0816

Gnomad4 OTH AF: 0.130

Alfa AF: 0.108 Hom.: 164

Bravo AF: 0.123

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.18
Dann	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs3767206; hg19: chr1-70715093; COSMIC: COSV63936814; COSMIC: COSV63936814;