chr8-127213195-G-A

Position:

• chr8-127213195-G-A

Variant summary

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

The ENST00000500112.2(CASC19):​n.430-3478C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,100 control chromosomes in the GnomAD database, including 3,622 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 0.22 (3622 hom., cov: 32)
• Consequence: CASC19 ENST00000500112.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

CASC19 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCAT1	NR_108049.1	n.460-3478C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC19	ENST00000500112.2	n.430-3478C>T		intron_variant		1
CASC19	ENST00000641001.1	n.154+5620C>T		intron_variant
CASC19	ENST00000641029.1	n.160+5615C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32680 AN: 151982 Hom.: 3616 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.215 AC: 32716 AN: 152100 Hom.: 3622 Cov.: 32 AF XY: 0.212 AC XY: 15788 AN XY: 74382

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.205

Alfa AF: 0.228 Hom.: 2730

Bravo AF: 0.206

Asia WGS AF: 0.186 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7816475; hg19: chr8-128225440;