rs2254177

Variant names:

• chr17-50281058-A-C
• rs2254177
• NM_153229.3:c.*1750A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-50281058-A-C
• chr17-50281058-A-G
• chr17-50281058-A-T

Variant summary

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

The NM_153229.3(TMEM92):​c.*1750A>C variant causes a 3 prime UTR 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: 31)
• Consequence: TMEM92 NM_153229.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 11 publications found

Genes affected

TMEM92 (HGNC:26579): (transmembrane protein 92) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TMEM92-AS1 (HGNC:50442): (TMEM92 antisense RNA 1)

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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM92	NM_153229.3	c.*1750A>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000507382.2	NP_694961.2
TMEM92	NM_001168215.2	c.*1750A>C		3_prime_UTR_variant	Exon 6 of 6		NP_001161687.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM92	ENST00000507382.2	c.*1750A>C		3_prime_UTR_variant	Exon 5 of 5	1	NM_153229.3	ENSP00000425144.1
TMEM92	ENST00000300433.7	c.*1750A>C		3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000300433.3
TMEM92-AS1	ENST00000784388.1	n.725T>G		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 124291

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.46
PhyloP100		0.17

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: rs2254177; hg19: chr17-48358419;