19-40347585-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001256441.2(C19orf47):​c.-34+739G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,918 control chromosomes in the GnomAD database, including 34,876 homozygotes. 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 0.68 (34876 hom., cov: 31)
• Consequence: C19orf47 NM_001256441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.54

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C19orf47	NM_001256441.2	c.-34+739G>A		intron_variant	Intron 1 of 8	ENST00000683109.1	NP_001243370.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C19orf47	ENST00000683109.1	c.-34+739G>A		intron_variant	Intron 1 of 8		NM_001256441.2	ENSP00000508349.1

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102838 AN: 151800 Hom.: 34865 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.677 AC: 102909 AN: 151918 Hom.: 34876 Cov.: 31 AF XY: 0.676 AC XY: 50190 AN XY: 74272

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.676

Alfa AF: 0.681 Hom.: 58972

Bravo AF: 0.680

Asia WGS AF: 0.726 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.055
DANN	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs7249146; hg19: chr19-40853492;