chr19-45052872-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007056.3. 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
	CLASRP	NM_007056.3	MANE Select	c.279C>T	p.Thr93Thr	synonymous	Exon 4 of 21	NP_008987.2	Q8N2M8-1
	CLASRP	NM_001278439.2		c.127-239C>T		intron	N/A	NP_001265368.1	Q8N2M8-4
	CLASRP	NR_103529.2		n.372C>T		non_coding_transcript_exon	Exon 4 of 21

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLASRP	ENST00000221455.8	TSL:1 MANE Select	c.279C>T	p.Thr93Thr	synonymous	Exon 4 of 21	ENSP00000221455.3	Q8N2M8-1
	CLASRP	ENST00000391952.7	TSL:1	n.279C>T		non_coding_transcript_exon	Exon 4 of 21	ENSP00000375814.2	Q8N2M8-3
	CLASRP	ENST00000587112.1	TSL:1	n.222C>T		non_coding_transcript_exon	Exon 3 of 11	ENSP00000466371.1	K7EM61

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

GnomAD2 exomes AF: 0.00532 AC: 1309 AN: 245926 AF XY: 0.00559

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 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

African (AFR) AF: 0.00117 AC: 39 AN: 33242

American (AMR) AF: 0.00876 AC: 382 AN: 43610

Ashkenazi Jewish (ASJ) AF: 0.000309 AC: 8 AN: 25918

East Asian (EAS) AF: 0.00 AC: 0 AN: 39662

South Asian (SAS) AF: 0.00477 AC: 410 AN: 85894

European-Finnish (FIN) AF: 0.00262 AC: 140 AN: 53374

Middle Eastern (MID) AF: 0.00227 AC: 13 AN: 5720

European-Non Finnish (NFE) AF: 0.00773 AC: 8587 AN: 1110518

Other (OTH) AF: 0.00630 AC: 379 AN: 60196

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

African (AFR) AF: 0.00128 AC: 53 AN: 41472

American (AMR) AF: 0.0121 AC: 184 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.00208 AC: 10 AN: 4818

European-Finnish (FIN) AF: 0.00198 AC: 21 AN: 10604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00824 AC: 560 AN: 67968

Other (OTH) AF: 0.0119 AC: 25 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.42
DANN	Benign	0.83
PhyloP100		-5.2
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

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