rs2614394

Variant names:

• chr12-43888363-A-G
• rs2614394
• NM_032256.3:c.277+43435A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-43888363-A-G
• chr12-43888363-A-T

Variant summary

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

The NM_032256.3(TMEM117):​c.277+43435A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,012 control chromosomes in the GnomAD database, including 49,074 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 0.78 (49074 hom., cov: 30)
• Consequence: TMEM117 NM_032256.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM117	NM_032256.3	c.277+43435A>G		intron_variant	Intron 2 of 7	ENST00000266534.8	NP_115632.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM117	ENST00000266534.8	c.277+43435A>G		intron_variant	Intron 2 of 7	1	NM_032256.3	ENSP00000266534.3
TMEM117	ENST00000551577.5	c.277+43435A>G		intron_variant	Intron 2 of 6	1		ENSP00000448595.1
TMEM117	ENST00000546868.5	n.277+43435A>G		intron_variant	Intron 2 of 6	1		ENSP00000446952.1
TMEM117	ENST00000550495.1	c.-23+43435A>G		intron_variant	Intron 1 of 5	5		ENSP00000448657.2

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118935 AN: 151894 Hom.: 49050 Cov.: 30

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.783 AC: 119003 AN: 152012 Hom.: 49074 Cov.: 30 AF XY: 0.786 AC XY: 58428 AN XY: 74312

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.818

Alfa AF: 0.848 Hom.: 10006

Bravo AF: 0.767

Asia WGS AF: 0.847 AC: 2946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.029
DANN	Benign	0.36

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: rs2614394; hg19: chr12-44282166;