rs13106655

Variant names:

• chr4-38990685-G-A
• rs13106655
• NM_024943.3:c.620-1715C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-38990685-G-A
• chr4-38990685-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024943.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM156	NM_024943.3	MANE Select	c.620-1715C>T		intron	N/A	NP_079219.1
	TMEM156	NM_001303228.2		c.620-1715C>T		intron	N/A	NP_001290157.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM156	ENST00000381938.4	TSL:1 MANE Select	c.620-1715C>T		intron	N/A	ENSP00000371364.3
	TMEM156	ENST00000850870.1		c.620-1715C>T		intron	N/A	ENSP00000520955.1

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

African (AFR) AF: 0.626 AC: 25871 AN: 41334

American (AMR) AF: 0.671 AC: 10222 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2175 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3665 AN: 5142

South Asian (SAS) AF: 0.599 AC: 2881 AN: 4806

European-Finnish (FIN) AF: 0.624 AC: 6539 AN: 10480

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42828 AN: 67918

Other (OTH) AF: 0.614 AC: 1290 AN: 2100

Alfa AF: 0.631 Hom.: 117642

Bravo AF: 0.637

Asia WGS AF: 0.673 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.6
DANN	Benign	0.74
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs13106655; hg19: chr4-38992305;