12-6471416-A-G

Variant names:

• chr12-6471416-A-G
• rs10492096
• XR_001748777.3:n.2713A>G

Variant summary

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

The XR_001748777.3(TAPBPL):​n.2713A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,978 control chromosomes in the GnomAD database, including 2,094 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 0.15 (2094 hom., cov: 32)
• Consequence: TAPBPL XR_001748777.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742

Genes affected

TAPBPL (HGNC:30683): (TAP binding protein like) Tapasin, or TAPBP (MIM 601962), is a member of the variable-constant Ig superfamily that links major histocompatibility complex (MHC) class I molecules to the transporter associated with antigen processing (TAP; see MIM 170260) in the endoplasmic reticulum (ER). The TAPBP gene is located near the MHC complex on chromosome 6p21.3. TAPBPL is a member of the Ig superfamily that is localized on chromosome 12p13.3, a region somewhat paralogous to the MHC.[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAPBPL	XR_001748777.3	n.2713A>G		non_coding_transcript_exon_variant	Exon 9 of 9
TAPBPL	XR_001748778.3	n.2710A>G		non_coding_transcript_exon_variant	Exon 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23290 AN: 151860 Hom.: 2096 Cov.: 32

Gnomad AFR AF: 0.0734

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00945

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.153 AC: 23294 AN: 151978 Hom.: 2094 Cov.: 32 AF XY: 0.152 AC XY: 11270 AN XY: 74264

Gnomad4 AFR AF: 0.0734

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00947

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.131

Alfa AF: 0.188 Hom.: 3756

Bravo AF: 0.144

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10492096; hg19: chr12-6580582;