rs4802073

Positions:

• chr19-40337357-A-G
• chr19-40337357-A-T

Variant summary

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

The NM_001256441.2(C19orf47):​c.20-950T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 149,704 control chromosomes in the GnomAD database, including 35,939 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 0.69 (35939 hom., cov: 25)
• Consequence: C19orf47 NM_001256441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

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=-0.99).
• 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/exons	MANE	UniProt
C19orf47	NM_001256441.2	c.20-950T>C		intron_variant		ENST00000683109.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C19orf47	ENST00000683109.1	c.20-950T>C		intron_variant			NM_001256441.2	P1

Frequencies

GnomAD3 genomes AF: 0.693 AC: 103658 AN: 149652 Hom.: 35933 Cov.: 25

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.693 AC: 103694 AN: 149704 Hom.: 35939 Cov.: 25 AF XY: 0.690 AC XY: 50354 AN XY: 72970

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.688

Alfa AF: 0.688 Hom.: 4245

Bravo AF: 0.697

Asia WGS AF: 0.728 AC: 2533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.44

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: rs4802073; hg19: chr19-40843264;