rs10520549

Variant names:

• chr2-97883349-A-G
• rs10520549
• NM_015348.2:c.359+4703T>C

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+4703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,108 control chromosomes in the GnomAD database, including 1,326 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 0.11 (1326 hom., cov: 32)
• Consequence: TMEM131 NM_015348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM131	NM_015348.2	c.359+4703T>C		intron_variant	Intron 4 of 40	ENST00000186436.10	NP_056163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM131	ENST00000186436.10	c.359+4703T>C		intron_variant	Intron 4 of 40	5	NM_015348.2	ENSP00000186436.5
TMEM131	ENST00000438715.1	c.20+4703T>C		intron_variant	Intron 2 of 4	4		ENSP00000411549.1
TMEM131	ENST00000418629.6	n.239+4703T>C		intron_variant	Intron 4 of 12	2		ENSP00000391566.2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16316 AN: 151990 Hom.: 1326 Cov.: 32

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.107 AC: 16316 AN: 152108 Hom.: 1326 Cov.: 32 AF XY: 0.109 AC XY: 8119 AN XY: 74348

African (AFR) AF: 0.0251 AC: 1042 AN: 41510

American (AMR) AF: 0.0730 AC: 1115 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4824

European-Finnish (FIN) AF: 0.261 AC: 2753 AN: 10546

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10604 AN: 67978

Other (OTH) AF: 0.0729 AC: 154 AN: 2112

Alfa AF: 0.127 Hom.: 3284

Bravo AF: 0.0900

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.37
PhyloP100		-0.47
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: rs10520549; hg19: chr2-98499812;