rs8105198

Variant names:

• chr19-48040605-G-A
• rs8105198
• NM_019855.5:c.238C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-48040605-G-A
• chr19-48040605-G-C
• chr19-48040605-G-T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_019855.5(CABP5):​c.238C>T​(p.Leu80Leu) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 1,613,232 control chromosomes in the GnomAD database, including 538,615 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.79 (47503 hom., cov: 30)
  • Exomes 𝑓: 0.82 (491112 hom.)
• Consequence: CABP5 NM_019855.5 splice_region, synonymous
• Scores: Splicing: ADA: 0.0001021
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 20 publications found

Genes affected

CABP5 (HGNC:13714): (calcium binding protein 5) The product of this gene belongs to a subfamily of calcium binding proteins, which share similarity to calmodulin. Calcium binding proteins are an important component of calcium mediated cellular signal transduction. Expression of this gene is retina-specific. The mouse homolog of this protein has been shown to express in the inner nuclear layer of the retina, suggested its role in neuronal functioning. The specific function of this gene is unknown. [provided by RefSeq, Oct 2009]

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BP7: Synonymous conserved (PhyloP=-0.632 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CABP5	NM_019855.5	c.238C>T	p.Leu80Leu	splice_region_variant, synonymous_variant	Exon 3 of 6	ENST00000293255.3	NP_062829.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CABP5	ENST00000293255.3	c.238C>T	p.Leu80Leu	splice_region_variant, synonymous_variant	Exon 3 of 6	1	NM_019855.5	ENSP00000293255.1

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119538 AN: 151866 Hom.: 47485 Cov.: 30

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.810

GnomAD2 exomes AF: 0.816 AC: 204933 AN: 251050 AF XY: 0.818

Gnomad AFR exome AF: 0.672

Gnomad AMR exome AF: 0.834

Gnomad ASJ exome AF: 0.759

Gnomad EAS exome AF: 0.863

Gnomad FIN exome AF: 0.863

Gnomad NFE exome AF: 0.821

Gnomad OTH exome AF: 0.825

GnomAD4 exome AF: 0.819 AC: 1197083 AN: 1461248 Hom.: 491112 Cov.: 47 AF XY: 0.819 AC XY: 595534 AN XY: 726946

African (AFR) AF: 0.677 AC: 22664 AN: 33460

American (AMR) AF: 0.835 AC: 37341 AN: 44702

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 19755 AN: 26100

East Asian (EAS) AF: 0.835 AC: 33153 AN: 39692

South Asian (SAS) AF: 0.807 AC: 69574 AN: 86218

European-Finnish (FIN) AF: 0.858 AC: 45802 AN: 53412

Middle Eastern (MID) AF: 0.833 AC: 4800 AN: 5760

European-Non Finnish (NFE) AF: 0.823 AC: 914695 AN: 1111546

Other (OTH) AF: 0.817 AC: 49299 AN: 60358

GnomAD4 genome AF: 0.787 AC: 119601 AN: 151984 Hom.: 47503 Cov.: 30 AF XY: 0.791 AC XY: 58760 AN XY: 74276

African (AFR) AF: 0.678 AC: 28087 AN: 41406

American (AMR) AF: 0.834 AC: 12740 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2570 AN: 3470

East Asian (EAS) AF: 0.855 AC: 4414 AN: 5162

South Asian (SAS) AF: 0.813 AC: 3908 AN: 4804

European-Finnish (FIN) AF: 0.864 AC: 9146 AN: 10586

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55927 AN: 67972

Other (OTH) AF: 0.809 AC: 1707 AN: 2110

Alfa AF: 0.810 Hom.: 161700

Bravo AF: 0.782

Asia WGS AF: 0.839 AC: 2920 AN: 3478

EpiCase AF: 0.822

EpiControl AF: 0.826

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.63
Mutation Taster		=67/33	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00010
dbscSNV1_RF	Benign	0.0
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: rs8105198; hg19: chr19-48543862; COSMIC: COSV53153545; COSMIC: COSV53153545;