rs1362378

Variant names:

• chr16-52272002-A-C
• rs1362378
• ENST00000569713.1:n.21-7607A>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000569713.1(CASC22):​n.21-7607A>C variant causes a intron 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 ENST00000569713.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 2 publications found

Genes affected

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

ENSG00000293674 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CASC22	NR_135281.1	n.21-7607A>C		intron_variant	Intron 1 of 2
LOC107983961	XR_007065214.1	n.279+132A>C		intron_variant	Intron 1 of 2
LOC107983961	XR_007065215.1	n.279+132A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CASC22	ENST00000569713.1	n.21-7607A>C		intron_variant	Intron 1 of 2	5
CASC22	ENST00000628396.1	n.299+132A>C		intron_variant	Intron 1 of 2	5
CASC22	ENST00000653084.1	n.305+132A>C		intron_variant	Intron 1 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 5 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.633 AC: 26178 AN: 41344

American (AMR) AF: 0.387 AC: 5906 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1559 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2805 AN: 5122

South Asian (SAS) AF: 0.351 AC: 1685 AN: 4804

European-Finnish (FIN) AF: 0.377 AC: 3961 AN: 10502

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26184 AN: 67896

Other (OTH) AF: 0.438 AC: 926 AN: 2114

Alfa AF: 0.458 Hom.: 2483

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1362378; hg19: chr16-52305914;