19-16496494-A-G

Position:

• chr19-16496494-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_032207.4(C19orf44):​c.-2+29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 315,416 control chromosomes in the GnomAD database, including 114,570 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.84 (54170 hom., cov: 30)
  • Exomes 𝑓: 0.86 (60400 hom.)
• Consequence: C19orf44 NM_032207.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.03

Genes affected

C19orf44 (HGNC:26141): (chromosome 19 open reading frame 44)

ENSG00000141979 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 19-16496494-A-G is Benign according to our data. Variant chr19-16496494-A-G is described in ClinVar as [Benign]. Clinvar id is 1243272.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C19orf44	NM_032207.4	c.-2+29A>G		intron_variant		ENST00000221671.8	NP_115583.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C19orf44	ENST00000221671.8	c.-2+29A>G		intron_variant		2	NM_032207.4	ENSP00000221671.2
ENSG00000141979	ENST00000409035.1	n.*380-642T>C		intron_variant		2		ENSP00000386951.2

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128047 AN: 151864 Hom.: 54120 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.865

GnomAD4 exome AF: 0.858 AC: 140215 AN: 163434 Hom.: 60400 Cov.: 0 AF XY: 0.861 AC XY: 76000 AN XY: 88232

Gnomad4 AFR exome AF: 0.796

Gnomad4 AMR exome AF: 0.871

Gnomad4 ASJ exome AF: 0.897

Gnomad4 EAS exome AF: 0.705

Gnomad4 SAS exome AF: 0.879

Gnomad4 FIN exome AF: 0.796

Gnomad4 NFE exome AF: 0.869

Gnomad4 OTH exome AF: 0.857

GnomAD4 genome AF: 0.843 AC: 128155 AN: 151982 Hom.: 54170 Cov.: 30 AF XY: 0.839 AC XY: 62316 AN XY: 74278

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.862

Alfa AF: 0.832 Hom.: 2635

Bravo AF: 0.846

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 10, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.9
DANN	Benign	0.50

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: rs3745325; hg19: chr19-16607305;