rs9321453

Variant names:

• chr6-134452416-T-C
• rs9321453
• ENST00000417483.5:n.316+2037A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-134452416-T-C
• chr6-134452416-T-G

Variant summary

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

The ENST00000417483.5(CT69):​n.316+2037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,034 control chromosomes in the GnomAD database, including 38,198 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 0.70 (38198 hom., cov: 32)
• Consequence: CT69 ENST00000417483.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 17 publications found

Genes affected

CT69 (HGNC:37196): (cancer/testis associated transcript 69)

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01010	NR_038216.1	n.167-12325T>C		intron_variant	Intron 1 of 2
LINC01010	NR_038217.1	n.167-12325T>C		intron_variant	Intron 1 of 2
LINC01010	NR_038218.1	n.133-12325T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CT69	ENST00000417483.5	n.316+2037A>G		intron_variant	Intron 3 of 4	3
CT69	ENST00000422736.2	n.261+2037A>G		intron_variant	Intron 3 of 5	3
LINC01010	ENST00000431422.3	n.621-12325T>C		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106637 AN: 151916 Hom.: 38163 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.702 AC: 106722 AN: 152034 Hom.: 38198 Cov.: 32 AF XY: 0.714 AC XY: 53013 AN XY: 74296

African (AFR) AF: 0.586 AC: 24269 AN: 41438

American (AMR) AF: 0.783 AC: 11967 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2196 AN: 3460

East Asian (EAS) AF: 0.997 AC: 5164 AN: 5180

South Asian (SAS) AF: 0.782 AC: 3770 AN: 4822

European-Finnish (FIN) AF: 0.829 AC: 8764 AN: 10578

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.710 AC: 48274 AN: 67964

Other (OTH) AF: 0.691 AC: 1460 AN: 2112

Alfa AF: 0.705 Hom.: 64222

Bravo AF: 0.694

Asia WGS AF: 0.877 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.32
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs9321453; hg19: chr6-134773554;