chr19-45052872-C-T

Variant names:

• chr19-45052872-C-T
• rs11667851
• NM_007056.3:c.279C>T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BP7 BS2

The NM_007056.3(CLASRP):​c.279C>T​(p.Thr93Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00672 in 1,610,216 control chromosomes in the GnomAD database, including 54 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. Synonymous variant affecting the same amino acid position (i.e. T93T) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0056 (6 hom., cov: 31)
  • Exomes 𝑓: 0.0068 (48 hom.)
• Consequence: CLASRP NM_007056.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.21

Genes affected

CLASRP (HGNC:17731): (CLK4 associating serine/arginine rich protein) Predicted to be involved in RNA splicing and mRNA processing. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP7: Synonymous conserved (PhyloP=-5.21 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLASRP	NM_007056.3	c.279C>T	p.Thr93Thr	synonymous_variant	Exon 4 of 21	ENST00000221455.8	NP_008987.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLASRP	ENST00000221455.8	c.279C>T	p.Thr93Thr	synonymous_variant	Exon 4 of 21	1	NM_007056.3	ENSP00000221455.3

Frequencies

GnomAD3 genomes AF: 0.00563 AC: 855 AN: 151964 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.00128

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0121

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00824

Gnomad OTH AF: 0.0120

GnomAD3 exomes AF: 0.00532 AC: 1309 AN: 245926 Hom.: 8 AF XY: 0.00559 AC XY: 745 AN XY: 133172

Gnomad AFR exome AF: 0.000930

Gnomad AMR exome AF: 0.00815

Gnomad ASJ exome AF: 0.000515

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00450

Gnomad FIN exome AF: 0.00187

Gnomad NFE exome AF: 0.00715

Gnomad OTH exome AF: 0.00771

GnomAD4 exome AF: 0.00683 AC: 9958 AN: 1458134 Hom.: 48 Cov.: 31 AF XY: 0.00674 AC XY: 4891 AN XY: 725524

Gnomad4 AFR exome AF: 0.00117

Gnomad4 AMR exome AF: 0.00876

Gnomad4 ASJ exome AF: 0.000309

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00477

Gnomad4 FIN exome AF: 0.00262

Gnomad4 NFE exome AF: 0.00773

Gnomad4 OTH exome AF: 0.00630

GnomAD4 genome AF: 0.00562 AC: 855 AN: 152082 Hom.: 6 Cov.: 31 AF XY: 0.00542 AC XY: 403 AN XY: 74352

Gnomad4 AFR AF: 0.00128

Gnomad4 AMR AF: 0.0121

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00208

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.00824

Gnomad4 OTH AF: 0.0119

Alfa AF: 0.00561 Hom.: 4

Bravo AF: 0.00633

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.42
DANN	Benign	0.83

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: rs11667851; hg19: chr19-45556130; COSMIC: COSV99674282; COSMIC: COSV99674282;