rs1053051

Variant names:

• chr12-106973447-T-C
• rs1053051
• NM_152261.4:c.*2056T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-106973447-T-C
• chr12-106973447-T-G

Variant summary

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

The NM_152261.4(TMEM263):​c.*2056T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 151,898 control chromosomes in the GnomAD database, including 29,342 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 0.61 (29284 hom., cov: 32)
  • Exomes 𝑓: 0.52 (58 hom.)
• Consequence: TMEM263 NM_152261.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 48 publications found

Genes affected

TMEM263 (HGNC:28281): (transmembrane protein 263) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

MTERF2 (HGNC:30779): (mitochondrial transcription termination factor 2) Enables DNA binding activity. Predicted to be involved in termination of mitochondrial transcription. Located in mitochondrion. [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=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM263	NM_152261.4	c.*2056T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000280756.9	NP_689474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM263	ENST00000280756.9	c.*2056T>C		3_prime_UTR_variant	Exon 4 of 4	1	NM_152261.4	ENSP00000280756.4

Frequencies

GnomAD3 genomes AF: 0.607 AC: 91817 AN: 151348 Hom.: 29235 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.583

GnomAD4 exome AF: 0.523 AC: 226 AN: 432 Hom.: 58 Cov.: 0 AF XY: 0.538 AC XY: 140 AN XY: 260

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.521 AC: 222 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.607 AC: 91921 AN: 151466 Hom.: 29284 Cov.: 32 AF XY: 0.611 AC XY: 45234 AN XY: 73998

African (AFR) AF: 0.793 AC: 32802 AN: 41362

American (AMR) AF: 0.670 AC: 10198 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2292 AN: 3450

East Asian (EAS) AF: 0.638 AC: 3263 AN: 5114

South Asian (SAS) AF: 0.614 AC: 2955 AN: 4816

European-Finnish (FIN) AF: 0.522 AC: 5462 AN: 10472

Middle Eastern (MID) AF: 0.552 AC: 160 AN: 290

European-Non Finnish (NFE) AF: 0.488 AC: 33032 AN: 67734

Other (OTH) AF: 0.580 AC: 1223 AN: 2108

Alfa AF: 0.534 Hom.: 85219

Bravo AF: 0.630

Asia WGS AF: 0.617 AC: 2140 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	14
DANN	Benign	0.65
PhyloP100		1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=98/2	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: rs1053051; hg19: chr12-107367225; COSMIC: COSV53527773; COSMIC: COSV53527773;