chr6-22656742-G-A

Variant names:

• chr6-22656742-G-A
• rs9348530
• XR_001744026.2:n.2530G>A

Variant summary

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

The XR_001744026.2(LOC105374973):​n.2530G>A 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 0.812 in 152,136 control chromosomes in the GnomAD database, including 50,533 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 0.81 (50533 hom., cov: 32)
• Consequence: LOC105374973 XR_001744026.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532
• Publications: 2 publications found

Genes affected

LOC105374973 (HGNC:):

CASC15 (HGNC:28245): (cancer susceptibility 15) This gene produces a long non-coding RNA that may regulate cell proliferation. This RNA is upregulated in hepatocellular carcinoma, where it is thought to function as an oncogene. However, some splice variants of this gene may function as a tumor suppressor in neuroblastoma and other tumor types. Circular RNA variants were observed at this gene. [provided by RefSeq, Dec 2017]

LINC03005 (HGNC:56130): (long intergenic non-protein coding RNA 3005)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374973	XR_001744026.2	n.2530G>A		non_coding_transcript_exon_variant	Exon 5 of 5
LOC105374973	XR_007059495.1	n.3350G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105374973	XR_007059496.1	n.2900G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03005	ENST00000821964.1	n.278-2038C>T		intron_variant	Intron 1 of 1
CASC15	ENST00000822125.1	n.513+730G>A		intron_variant	Intron 4 of 4
CASC15	ENST00000822127.1	n.228+730G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123408 AN: 152018 Hom.: 50491 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.812 AC: 123507 AN: 152136 Hom.: 50533 Cov.: 32 AF XY: 0.813 AC XY: 60456 AN XY: 74364

African (AFR) AF: 0.903 AC: 37532 AN: 41544

American (AMR) AF: 0.852 AC: 13029 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2599 AN: 3468

East Asian (EAS) AF: 0.651 AC: 3360 AN: 5160

South Asian (SAS) AF: 0.802 AC: 3861 AN: 4816

European-Finnish (FIN) AF: 0.782 AC: 8272 AN: 10580

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52065 AN: 67968

Other (OTH) AF: 0.802 AC: 1693 AN: 2110

Alfa AF: 0.799 Hom.: 8479

Bravo AF: 0.823

Asia WGS AF: 0.735 AC: 2559 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.63
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs9348530; hg19: chr6-22656971;