rs1726886

Variant names:

• chr12-44328993-G-A
• rs1726886
• NM_032256.3:c.768+29254G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-44328993-G-A
• chr12-44328993-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032256.3(TMEM117):​c.768+29254G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 151,112 control chromosomes in the GnomAD database, including 34,980 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 0.67 (34980 hom., cov: 27)
• Consequence: TMEM117 NM_032256.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 3 publications found

Genes affected

TMEM117 (HGNC:25308): (transmembrane protein 117) Involved in intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress. Located in endoplasmic reticulum and plasma 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM117	NM_032256.3	c.768+29254G>A		intron_variant	Intron 6 of 7	ENST00000266534.8	NP_115632.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM117	ENST00000266534.8	c.768+29254G>A		intron_variant	Intron 6 of 7	1	NM_032256.3	ENSP00000266534.3

Frequencies

GnomAD3 genomes AF: 0.667 AC: 100651 AN: 150994 Hom.: 34921 Cov.: 27

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.667 AC: 100767 AN: 151112 Hom.: 34980 Cov.: 27 AF XY: 0.672 AC XY: 49556 AN XY: 73746

African (AFR) AF: 0.848 AC: 34951 AN: 41230

American (AMR) AF: 0.714 AC: 10790 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2381 AN: 3464

East Asian (EAS) AF: 0.895 AC: 4551 AN: 5084

South Asian (SAS) AF: 0.711 AC: 3372 AN: 4742

European-Finnish (FIN) AF: 0.547 AC: 5687 AN: 10402

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36875 AN: 67784

Other (OTH) AF: 0.659 AC: 1387 AN: 2104

Alfa AF: 0.598 Hom.: 5833

Bravo AF: 0.687

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		-0.26
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: rs1726886; hg19: chr12-44722776;