rs1026015

Variant names:

• chr2-97883754-T-C
• rs1026015
• NM_015348.2:c.359+4298A>G

Variant summary

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

The NM_015348.2(TMEM131):​c.359+4298A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0292 in 152,230 control chromosomes in the GnomAD database, including 78 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 0.029 (78 hom., cov: 32)
• Consequence: TMEM131 NM_015348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 2 publications found

Genes affected

TMEM131 (HGNC:30366): (transmembrane protein 131) Predicted to be integral component of membrane. Predicted to be active in 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015348.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM131	NM_015348.2	MANE Select	c.359+4298A>G		intron	N/A	NP_056163.1	Q92545

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM131	ENST00000186436.10	TSL:5 MANE Select	c.359+4298A>G		intron	N/A	ENSP00000186436.5	Q92545
	TMEM131	ENST00000962018.1		c.410+4298A>G		intron	N/A	ENSP00000632077.1
	TMEM131	ENST00000913347.1		c.359+4298A>G		intron	N/A	ENSP00000583406.1

Frequencies

GnomAD3 genomes AF: 0.0292 AC: 4438 AN: 152114 Hom.: 78 Cov.: 32

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.00659

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0417

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

GnomAD4 genome AF: 0.0292 AC: 4439 AN: 152230 Hom.: 78 Cov.: 32 AF XY: 0.0283 AC XY: 2110 AN XY: 74434

African (AFR) AF: 0.0545 AC: 2264 AN: 41516

American (AMR) AF: 0.0239 AC: 365 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.00332 AC: 16 AN: 4824

European-Finnish (FIN) AF: 0.00659 AC: 70 AN: 10616

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0215 AC: 1462 AN: 68014

Other (OTH) AF: 0.0412 AC: 87 AN: 2110

Alfa AF: 0.0284 Hom.: 4

Bravo AF: 0.0327

Asia WGS AF: 0.00667 AC: 23 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.82
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism

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: rs1026015; hg19: chr2-98500217;