rs10498703

Positions:

• chr6-22018598-G-A
• chr6-22018598-G-C

Variant summary

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

The NR_015410.2(CASC15):​n.900-1741G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 151,932 control chromosomes in the GnomAD database, including 1,900 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 0.13 (1900 hom., cov: 32)
• Consequence: CASC15 NR_015410.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

Genes affected

CASC15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CASC15	NR_015410.2	n.900-1741G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CASC15	ENST00000444265.6	n.318-1741G>A		intron_variant		1
CASC15	ENST00000606851.5	n.869-1741G>A		intron_variant		2
CASC15	ENST00000607048.5	n.495-1741G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19884 AN: 151814 Hom.: 1892 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.131 AC: 19916 AN: 151932 Hom.: 1900 Cov.: 32 AF XY: 0.136 AC XY: 10108 AN XY: 74240

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0932

Gnomad4 NFE AF: 0.0888

Gnomad4 OTH AF: 0.131

Alfa AF: 0.134 Hom.: 698

Bravo AF: 0.146

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498703; hg19: chr6-22018827;