5-83076927-C-T

Variant names:

• chr5-83076927-C-T
• rs2075686
• NM_174909.5:c.3+394G>A

Variant summary

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

The NM_174909.5(TMEM167A):​c.3+394G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 152,228 control chromosomes in the GnomAD database, including 325 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 0.021 (325 hom., cov: 33)
• Consequence: TMEM167A NM_174909.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

Genes affected

TMEM167A (HGNC:28330): (transmembrane protein 167A) Involved in constitutive secretory pathway. Located in Golgi apparatus. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM167A	NM_174909.5	c.3+394G>A		intron_variant	Intron 1 of 3	ENST00000502346.2	NP_777569.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM167A	ENST00000502346.2	c.3+394G>A		intron_variant	Intron 1 of 3	1	NM_174909.5	ENSP00000424707.1

Frequencies

GnomAD3 genomes AF: 0.0209 AC: 3180 AN: 152110 Hom.: 325 Cov.: 33

Gnomad AFR AF: 0.00128

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0590

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00103

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0209 AC: 3174 AN: 152228 Hom.: 325 Cov.: 33 AF XY: 0.0254 AC XY: 1887 AN XY: 74436

Gnomad4 AFR AF: 0.00128

Gnomad4 AMR AF: 0.0588

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.0337

Gnomad4 NFE AF: 0.00103

Gnomad4 OTH AF: 0.0189

Alfa AF: 0.00741 Hom.: 13

Bravo AF: 0.0229

Asia WGS AF: 0.0960 AC: 335 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	1.4
DANN	Benign	0.47

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: rs2075686; hg19: chr5-82372746;