rs7249146

Variant names:

• chr19-40347585-C-A
• rs7249146
• NM_001256441.2:c.-34+739G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-40347585-C-A
• chr19-40347585-C-T

Variant summary

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

The NM_001256441.2(C19orf47):​c.-34+739G>T 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: 31)
• Consequence: C19orf47 NM_001256441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54
• Publications: 11 publications found

Genes affected

C19orf47 (HGNC:26723): (chromosome 19 open reading frame 47) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256441.2. 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
	C19orf47	NM_001256441.2	MANE Select	c.-34+739G>T		intron	N/A	NP_001243370.1	A0A804HLH2
	C19orf47	NM_001256440.1		c.78+852G>T		intron	N/A	NP_001243369.1	Q8N9M1-1
	C19orf47	NR_046202.2		n.74+739G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C19orf47	ENST00000683109.1	MANE Select	c.-34+739G>T		intron	N/A	ENSP00000508349.1	A0A804HLH2
	C19orf47	ENST00000582783.5	TSL:1	c.78+852G>T		intron	N/A	ENSP00000463159.1	Q8N9M1-1
	C19orf47	ENST00000392035.6	TSL:1	c.-177+739G>T		intron	N/A	ENSP00000375889.2	Q8N9M1-2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 133142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.039
DANN	Benign	0.39
PhyloP100		-3.5

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: rs7249146; hg19: chr19-40853492;