rs8019166

Variant names:

• chr14-69773209-C-T
• rs8019166
• ENST00000880757.1:c.*1748C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000880757.1(SRSF5):​c.*1748C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,220 control chromosomes in the GnomAD database, including 1,678 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 0.13 (1678 hom., cov: 32)
• Consequence: SRSF5 ENST00000880757.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 5 publications found

Genes affected

SRSF5 (HGNC:10787): (serine and arginine rich splicing factor 5) The protein encoded by this gene is a member of the serine/arginine (SR)-rich family of pre-mRNA splicing factors, which constitute part of the spliceosome. Each of these factors contains an RNA recognition motif (RRM) for binding RNA and an RS domain for binding other proteins. The RS domain is rich in serine and arginine residues and facilitates interaction between different SR splicing factors. In addition to being critical for mRNA splicing, the SR proteins have also been shown to be involved in mRNA export from the nucleus and in translation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000880757.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRSF5	ENST00000880757.1		c.*1748C>T		3_prime_UTR	Exon 9 of 9	ENSP00000550816.1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19315 AN: 152102 Hom.: 1674 Cov.: 32

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.127 AC: 19334 AN: 152220 Hom.: 1678 Cov.: 32 AF XY: 0.128 AC XY: 9538 AN XY: 74424

African (AFR) AF: 0.0334 AC: 1389 AN: 41546

American (AMR) AF: 0.201 AC: 3078 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3470

East Asian (EAS) AF: 0.00616 AC: 32 AN: 5192

South Asian (SAS) AF: 0.0362 AC: 175 AN: 4828

European-Finnish (FIN) AF: 0.206 AC: 2175 AN: 10568

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11574 AN: 68008

Other (OTH) AF: 0.141 AC: 298 AN: 2112

Alfa AF: 0.157 Hom.: 457

Bravo AF: 0.124

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.54
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs8019166; hg19: chr14-70239926;