chr17-18800718-G-A

Variant names:

• chr17-18800718-G-A
• rs11871508
• NM_016078.6:c.462+1775G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_016078.6(TVP23B):​c.462+1775G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0163 in 151,890 control chromosomes in the GnomAD database, including 28 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 0.016 (28 hom., cov: 30)
• Consequence: TVP23B NM_016078.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 3 publications found

Genes affected

TVP23B (HGNC:20399): (trans-golgi network vesicle protein 23 homolog B) Predicted to be involved in protein secretion and vesicle-mediated transport. Predicted to be integral component of membrane. Predicted to be integral component of Golgi 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=-0.96).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0163 (2473/151890) while in subpopulation NFE AF = 0.0249 (1689/67930). AF 95% confidence interval is 0.0239. There are 28 homozygotes in GnomAd4. There are 1155 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TVP23B	NM_016078.6	c.462+1775G>A		intron_variant	Intron 5 of 6	ENST00000307767.13	NP_057162.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TVP23B	ENST00000307767.13	c.462+1775G>A		intron_variant	Intron 5 of 6	1	NM_016078.6	ENSP00000305654.8

Frequencies

GnomAD3 genomes AF: 0.0163 AC: 2477 AN: 151772 Hom.: 28 Cov.: 30

Gnomad AFR AF: 0.00484

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0148

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0127

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0249

Gnomad OTH AF: 0.0231

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

GnomAD4 genome AF: 0.0163 AC: 2473 AN: 151890 Hom.: 28 Cov.: 30 AF XY: 0.0156 AC XY: 1155 AN XY: 74244

African (AFR) AF: 0.00483 AC: 200 AN: 41430

American (AMR) AF: 0.0147 AC: 225 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5162

South Asian (SAS) AF: 0.0125 AC: 60 AN: 4800

European-Finnish (FIN) AF: 0.0125 AC: 131 AN: 10516

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0249 AC: 1689 AN: 67930

Other (OTH) AF: 0.0229 AC: 48 AN: 2100

Alfa AF: 0.0178 Hom.: 5

Bravo AF: 0.0163

Asia WGS AF: 0.00463 AC: 16 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		0.064
Mutation Taster		=100/0	polymorphism

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: rs11871508; hg19: chr17-18704031;