rs13050999

Variant names:

• chr21-44424718-C-A
• rs13050999
• NM_003307.4:c.3550-134C>A

Your query was ambiguous. Multiple possible variants found:

• chr21-44424718-C-A
• chr21-44424718-C-G
• chr21-44424718-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003307.4(TRPM2):​c.3550-134C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TRPM2 NM_003307.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 2 publications found

Genes affected

TRPM2 (HGNC:12339): (transient receptor potential cation channel subfamily M member 2) The protein encoded by this gene forms a tetrameric cation channel that is permeable to calcium, sodium, and potassium and is regulated by free intracellular ADP-ribose. The encoded protein is activated by oxidative stress and confers susceptibility to cell death. Alternative splicing results in multiple transcript variants encoding distinct protein isoforms. Additional transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Feb 2016]

TRPM2-AS (HGNC:50758): (TRPM2 antisense RNA)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003307.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPM2	NM_003307.4	MANE Select	c.3550-134C>A		intron	N/A	NP_003298.2	O94759-1
	TRPM2	NM_001320350.2		c.3700-134C>A		intron	N/A	NP_001307279.2	E9PGK7
	TRPM2	NM_001433516.1		c.3550-134C>A		intron	N/A	NP_001420445.1	O94759-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPM2	ENST00000397928.6	TSL:1 MANE Select	c.3550-134C>A		intron	N/A	ENSP00000381023.1	O94759-1
	TRPM2	ENST00000397932.6	TSL:1	c.3700-134C>A		intron	N/A	ENSP00000381026.2	E9PGK7
	TRPM2	ENST00000300482.9	TSL:1	c.3550-134C>A		intron	N/A	ENSP00000300482.5	O94759-1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 395464 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 204226

African (AFR) AF: 0.00 AC: 0 AN: 10190

American (AMR) AF: 0.00 AC: 0 AN: 11998

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11126

East Asian (EAS) AF: 0.00 AC: 0 AN: 24860

South Asian (SAS) AF: 0.00 AC: 0 AN: 25046

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26062

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1990

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 262198

Other (OTH) AF: 0.00 AC: 0 AN: 21994

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 5959

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.65
PhyloP100		1.8

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: rs13050999; hg19: chr21-45844601;