rs1021955

Positions:

• chr8-127191728-A-G
• chr8-127191728-A-T

Variant summary

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

The ENST00000641060.1(CASC19):​n.442T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,950 control chromosomes in the GnomAD database, including 17,657 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 0.46 (17657 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CASC19 ENST00000641060.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.749

Genes affected

CASC19 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC19	NR_120364.1	n.154-3613T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC19	ENST00000641060.1	n.442T>C		non_coding_transcript_exon_variant	5/7
CASC19	ENST00000641674.2	n.538T>C		non_coding_transcript_exon_variant	5/9
CASC19	ENST00000642082.1	n.588T>C		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69886 AN: 151830 Hom.: 17619 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.422

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 SAS exome AF: 0.00

GnomAD4 genome AF: 0.461 AC: 69977 AN: 151950 Hom.: 17657 Cov.: 31 AF XY: 0.454 AC XY: 33723 AN XY: 74248

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.423

Alfa AF: 0.414 Hom.: 4163

Bravo AF: 0.479

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.57
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1021955; hg19: chr8-128203973;