1-15177907-T-G

Position:

• chr1-15177907-T-G

Variant summary

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

The NM_001136218.2(TMEM51):​c.-267+23953T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,956 control chromosomes in the GnomAD database, including 11,649 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 0.36 (11649 hom., cov: 32)
• Consequence: TMEM51 NM_001136218.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

Genes affected

TMEM51 (HGNC:25488): (transmembrane protein 51) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM51 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM51	NM_001136218.2	c.-267+23953T>G		intron_variant		ENST00000376008.3	NP_001129690.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM51	ENST00000376008.3	c.-267+23953T>G		intron_variant		2	NM_001136218.2	ENSP00000365176.1

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55404 AN: 151838 Hom.: 11635 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.365 AC: 55430 AN: 151956 Hom.: 11649 Cov.: 32 AF XY: 0.370 AC XY: 27510 AN XY: 74260

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.398

Alfa AF: 0.428 Hom.: 29110

Bravo AF: 0.365

Asia WGS AF: 0.496 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.14
DANN	Benign	0.57

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: rs10927698; hg19: chr1-15504403;