rs17379636

chr4-153485526-A-Gchr4-153485526-A-T

Variant summary

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

The NM_001131007.2(TMEM131L):c.239+11638A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,976 control chromosomes in the GnomAD database, including 19,568 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 0.49 (19568 hom., cov: 32)
• Consequence: TMEM131L NM_001131007.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

Genes affected

TMEM131L (HGNC:29146): (transmembrane 131 like) Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of immature T cell proliferation in thymus. Located in cytoplasm 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM131L	NM_001131007.2	c.239+11638A>G		intron_variant		ENST00000409959.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM131L	ENST00000409959.8	c.239+11638A>G		intron_variant		5	NM_001131007.2	A2
TMEM131L	ENST00000409663.7	c.239+11638A>G		intron_variant		5		P4
TMEM131L	ENST00000445960.5	c.195+18245A>G		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74877 AN: 151858 Hom.: 19544 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.493 AC: 74948 AN: 151976 Hom.: 19568 Cov.: 32 AF XY: 0.496 AC XY: 36857 AN XY: 74268

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.475

Alfa AF: 0.430 Hom.: 6858

Bravo AF: 0.506

Asia WGS AF: 0.623 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	14
Dann	Benign	0.80

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: rs17379636; hg19: chr4-154406678;