rs1362378

Positions:

• chr16-52272002-A-C
• chr16-52272002-A-G

Variant summary

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

The NR_135281.1(CASC22):​n.21-7607A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,720 control chromosomes in the GnomAD database, including 16,986 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 (16986 hom., cov: 31)
  • Exomes 𝑓: 0.42 (0 hom.)
• Consequence: CASC22 NR_135281.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

CASC22 (HGNC:50627): (cancer susceptibility 22)

LOC107983961 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASC22	NR_135281.1	n.21-7607A>C		intron_variant, non_coding_transcript_variant
LOC107983961	XR_007065214.1	n.279+132A>C		intron_variant, non_coding_transcript_variant
LOC107983961	XR_007065215.1	n.279+132A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASC22	ENST00000569713.1	n.21-7607A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69527 AN: 151588 Hom.: 16946 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.444

GnomAD4 exome AF: 0.417 AC: 5 AN: 12 Hom.: 0 AF XY: 0.400 AC XY: 4 AN XY: 10

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.459 AC: 69616 AN: 151708 Hom.: 16986 Cov.: 31 AF XY: 0.453 AC XY: 33548 AN XY: 74072

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.438

Alfa AF: 0.451 Hom.: 2319

Bravo AF: 0.471

Asia WGS AF: 0.413 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1362378; hg19: chr16-52305914;