13-51817205-C-T

Variant names:

• chr13-51817205-C-T
• rs975504
• NM_001351003.2:c.202-92G>A

Variant summary

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

The NM_001351003.2(TMEM272):​c.202-92G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 620,672 control chromosomes in the GnomAD database, including 154,034 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 0.70 (37356 hom., cov: 30)
  • Exomes 𝑓: 0.70 (116678 hom.)
• Consequence: TMEM272 NM_001351003.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 4 publications found

Genes affected

TMEM272 (HGNC:26737): (transmembrane protein 272) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285444 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM272	NM_001351003.2	c.202-92G>A		intron_variant	Intron 4 of 4	ENST00000629372.3	NP_001337932.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM272	ENST00000629372.3	c.202-92G>A		intron_variant	Intron 4 of 4	4	NM_001351003.2	ENSP00000490718.2
ENSG00000285444	ENST00000642706.1	n.59-3866G>A		intron_variant	Intron 2 of 10			ENSP00000495561.1
TMEM272	ENST00000626362.3	c.119-92G>A		intron_variant	Intron 3 of 3	4		ENSP00000489719.2
TMEM272	ENST00000627246.3	c.59-92G>A		intron_variant	Intron 2 of 2	2		ENSP00000490137.2

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106031 AN: 151600 Hom.: 37340 Cov.: 30

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.718

GnomAD4 exome AF: 0.700 AC: 328111 AN: 468950 Hom.: 116678 AF XY: 0.698 AC XY: 172936 AN XY: 247588

African (AFR) AF: 0.661 AC: 8832 AN: 13364

American (AMR) AF: 0.744 AC: 17976 AN: 24164

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 10640 AN: 14770

East Asian (EAS) AF: 0.411 AC: 12853 AN: 31242

South Asian (SAS) AF: 0.665 AC: 33057 AN: 49736

European-Finnish (FIN) AF: 0.694 AC: 21142 AN: 30446

Middle Eastern (MID) AF: 0.702 AC: 2564 AN: 3652

European-Non Finnish (NFE) AF: 0.736 AC: 202128 AN: 274574

Other (OTH) AF: 0.701 AC: 18919 AN: 27002

GnomAD4 genome AF: 0.699 AC: 106092 AN: 151722 Hom.: 37356 Cov.: 30 AF XY: 0.695 AC XY: 51524 AN XY: 74120

African (AFR) AF: 0.655 AC: 27053 AN: 41310

American (AMR) AF: 0.739 AC: 11287 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2530 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2411 AN: 5146

South Asian (SAS) AF: 0.653 AC: 3135 AN: 4802

European-Finnish (FIN) AF: 0.684 AC: 7195 AN: 10512

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50020 AN: 67904

Other (OTH) AF: 0.716 AC: 1505 AN: 2102

Alfa AF: 0.726 Hom.: 20323

Bravo AF: 0.702

Asia WGS AF: 0.608 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.48
PhyloP100		-3.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.99

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs975504; hg19: chr13-52391341; COSMIC: COSV71749195; COSMIC: COSV71749195;