rs6981122

Positions:

• chr8-127082215-A-C
• chr8-127082215-A-T

Variant summary

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

The ENST00000523510.1(CASC19):​n.7T>G 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 0.581 in 151,950 control chromosomes in the GnomAD database, including 26,369 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 0.58 (26369 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CASC19 ENST00000523510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

CASC19 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRNCR1	NR_109833.1	n.2342A>C		non_coding_transcript_exon_variant	1/1
PCAT2	NR_119373.1	n.7T>G		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC19	ENST00000523510.1	n.7T>G		non_coding_transcript_exon_variant	1/4	3
PRNCR1	ENST00000635449.1	n.2342A>C		non_coding_transcript_exon_variant	1/1	6
CASC19	ENST00000641794.1	n.68T>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88249 AN: 151832 Hom.: 26345 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.581 AC: 88318 AN: 151950 Hom.: 26369 Cov.: 32 AF XY: 0.570 AC XY: 42305 AN XY: 74262

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.568

Alfa AF: 0.558 Hom.: 23326

Bravo AF: 0.583

Asia WGS AF: 0.502 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6981122; hg19: chr8-128094460;