chr19-44958739-A-G

Variant names:

• chr19-44958739-A-G
• rs204907
• NM_001294.4:c.73-3224A>G

Variant summary

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

The NM_001294.4(CLPTM1):​c.73-3224A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 152,214 control chromosomes in the GnomAD database, including 688 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 0.084 (688 hom., cov: 32)
• Consequence: CLPTM1 NM_001294.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLPTM1	NM_001294.4	c.73-3224A>G		intron_variant	Intron 1 of 13	ENST00000337392.10	NP_001285.1
CLPTM1	NM_001282175.2	c.31-3224A>G		intron_variant	Intron 1 of 13		NP_001269104.1
CLPTM1	NM_001282176.2	c.-234-3224A>G		intron_variant	Intron 1 of 13		NP_001269105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLPTM1	ENST00000337392.10	c.73-3224A>G		intron_variant	Intron 1 of 13	1	NM_001294.4	ENSP00000336994.4

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12766 AN: 152096 Hom.: 685 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.0515

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0840 AC: 12787 AN: 152214 Hom.: 688 Cov.: 32 AF XY: 0.0832 AC XY: 6191 AN XY: 74428

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.0795

Gnomad4 SAS AF: 0.0511

Gnomad4 FIN AF: 0.0354

Gnomad4 NFE AF: 0.0495

Gnomad4 OTH AF: 0.0860

Alfa AF: 0.0608 Hom.: 225

Bravo AF: 0.0928

Asia WGS AF: 0.0810 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0070
DANN	Benign	0.65

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: rs204907; hg19: chr19-45461996;