rs975504

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-51817205-C-G
• chr13-51817205-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001351003.2(TMEM272):​c.202-92G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 151684 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 469114 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 247668

African (AFR) AF: 0.00 AC: 0 AN: 13366

American (AMR) AF: 0.00 AC: 0 AN: 24172

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14784

East Asian (EAS) AF: 0.00 AC: 0 AN: 31246

South Asian (SAS) AF: 0.00 AC: 0 AN: 49768

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30456

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3652

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 274660

Other (OTH) AF: 0.00 AC: 0 AN: 27010

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 151684 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 74036

African (AFR) AF: 0.00 AC: 0 AN: 41218

American (AMR) AF: 0.00 AC: 0 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.00 AC: 0 AN: 4810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10518

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67936

Other (OTH) AF: 0.00 AC: 0 AN: 2084

Alfa AF: 0.00 Hom.: 20323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.32
DANN	Benign	0.42
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;