rs1026015

chr2-97883754-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM131	NM_015348.2	c.359+4298A>G		intron_variant		ENST00000186436.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM131	ENST00000186436.10	c.359+4298A>G		intron_variant		5	NM_015348.2	P1
TMEM131	ENST00000438715.1	c.20+4298A>G		intron_variant		4
TMEM131	ENST00000418629.6	c.241+4298A>G		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.0239

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00332

Gnomad4 FIN AF: 0.00659

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0267 Hom.: 4

Bravo AF: 0.0327

Asia WGS AF: 0.00667 AC: 23 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.82

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: rs1026015; hg19: chr2-98500217;