rs6869366

chr5-83075927-T-G

Variant summary

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

The NM_174909.5(TMEM167A):c.3+1394A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0918 in 152,160 control chromosomes in the GnomAD database, including 868 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 0.092 (868 hom., cov: 32)
• Consequence: TMEM167A NM_174909.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM167A	NM_174909.5	c.3+1394A>C		intron_variant		ENST00000502346.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM167A	ENST00000502346.2	c.3+1394A>C		intron_variant		1	NM_174909.5	P1

Frequencies

GnomAD3 genomes AF: 0.0919 AC: 13966 AN: 152042 Hom.: 867 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0766

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.0918 AC: 13973 AN: 152160 Hom.: 868 Cov.: 32 AF XY: 0.0929 AC XY: 6908 AN XY: 74398

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.0768

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0738 Hom.: 76

Bravo AF: 0.0913

Asia WGS AF: 0.134 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	8.8
Dann	Benign	0.77

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: rs6869366; hg19: chr5-82371746;