rs16979595

Variant names:

• chr19-44974124-G-A
• rs16979595
• NM_001294.4:c.310-315G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001294.4(CLPTM1):​c.310-315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,734 control chromosomes in the GnomAD database, including 2,922 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 0.19 (2922 hom., cov: 31)
• Consequence: CLPTM1 NM_001294.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 26 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001294.4. 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
	CLPTM1	NM_001294.4	MANE Select	c.310-315G>A		intron	N/A	NP_001285.1
	CLPTM1	NM_001282175.2		c.268-315G>A		intron	N/A	NP_001269104.1
	CLPTM1	NM_001282176.2		c.4-315G>A		intron	N/A	NP_001269105.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPTM1	ENST00000337392.10	TSL:1 MANE Select	c.310-315G>A		intron	N/A	ENSP00000336994.4
	CLPTM1	ENST00000588855.5	TSL:1	n.355-315G>A		intron	N/A
	CLPTM1	ENST00000870268.1		c.310-315G>A		intron	N/A	ENSP00000540327.1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28879 AN: 151616 Hom.: 2923 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0553

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.190 AC: 28900 AN: 151734 Hom.: 2922 Cov.: 31 AF XY: 0.192 AC XY: 14229 AN XY: 74166

African (AFR) AF: 0.214 AC: 8837 AN: 41378

American (AMR) AF: 0.203 AC: 3093 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 820 AN: 3458

East Asian (EAS) AF: 0.271 AC: 1388 AN: 5124

South Asian (SAS) AF: 0.195 AC: 935 AN: 4806

European-Finnish (FIN) AF: 0.194 AC: 2047 AN: 10544

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11276 AN: 67878

Other (OTH) AF: 0.190 AC: 400 AN: 2106

Alfa AF: 0.178 Hom.: 6502

Bravo AF: 0.193

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.8
DANN	Benign	0.44
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

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: rs16979595; hg19: chr19-45477381;