ENST00000452922.5:n.808+2253C>G

Variant names:

• chr1-94677172-G-C
• rs841338
• ENST00000452922.5:n.808+2253C>G

Variant summary

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

The ENST00000452922.5(SLC44A3-AS1):​n.808+2253C>G 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: 32)
• Consequence: SLC44A3-AS1 ENST00000452922.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 4 publications found

Genes affected

SLC44A3-AS1 (HGNC:):

SLC44A3-AS1 (HGNC:49057): (SLC44A3 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=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452922.5. 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
	SLC44A3-AS1	NR_104131.2		n.759+2253C>G		intron	N/A
	SLC44A3-AS1	NR_160779.1		n.512+2253C>G		intron	N/A
	SLC44A3-AS1	NR_160780.1		n.640+2253C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3-AS1	ENST00000452922.5	TSL:1	n.808+2253C>G		intron	N/A
	SLC44A3-AS1	ENST00000414374.2	TSL:3	n.438+2253C>G		intron	N/A
	SLC44A3-AS1	ENST00000421997.5	TSL:3	n.566+2253C>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 41381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.57
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs841338; hg19: chr1-95142728;