rs13106655

chr4-38990685-G-Achr4-38990685-G-C

Variant summary

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

The NM_024943.3(TMEM156):c.620-1715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,686 control chromosomes in the GnomAD database, including 30,452 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 0.63 (30452 hom., cov: 29)
• Consequence: TMEM156 NM_024943.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

TMEM156 (HGNC:26260): (transmembrane protein 156) Predicted to be integral component of membrane. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM156	NM_024943.3	c.620-1715C>T		intron_variant		ENST00000381938.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM156	ENST00000381938.4	c.620-1715C>T		intron_variant		1	NM_024943.3	P1

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96053 AN: 151568 Hom.: 30431 Cov.: 29

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.634 AC: 96127 AN: 151686 Hom.: 30452 Cov.: 29 AF XY: 0.632 AC XY: 46840 AN XY: 74076

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.614

Alfa AF: 0.629 Hom.: 50313

Bravo AF: 0.637

Asia WGS AF: 0.673 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	7.6
Dann	Benign	0.74

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: rs13106655; hg19: chr4-38992305;