rs8111069

chr19-44980181-A-Cchr19-44980181-A-T

Variant summary

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

The NM_001294.4(CLPTM1):c.586+2721A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,910 control chromosomes in the GnomAD database, including 11,949 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 0.39 (11949 hom., cov: 31)
• Consequence: CLPTM1 NM_001294.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

Genes affected

CLPTM1 (HGNC:2087): (CLPTM1 regulator of GABA type A receptor forward trafficking) Predicted to be involved in regulation of T cell differentiation in thymus. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLPTM1	NM_001294.4	c.586+2721A>C		intron_variant		ENST00000337392.10
CLPTM1	NM_001282175.2	c.544+2721A>C		intron_variant
CLPTM1	NM_001282176.2	c.280+2721A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLPTM1	ENST00000337392.10	c.586+2721A>C		intron_variant		1	NM_001294.4	P1

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58820 AN: 151792 Hom.: 11925 Cov.: 31

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.388 AC: 58899 AN: 151910 Hom.: 11949 Cov.: 31 AF XY: 0.390 AC XY: 28919 AN XY: 74226

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.387

Alfa AF: 0.339 Hom.: 13006

Bravo AF: 0.397

Asia WGS AF: 0.428 AC: 1491 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	0.55
Dann	Benign	0.57

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: rs8111069; hg19: chr19-45483438;