rs9321453

Positions:

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

Variant summary

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

The NR_038216.1(LINC01010):​n.167-12325T>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 0.702 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: LINC01010 NR_038216.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01010	NR_038216.1	n.167-12325T>C		intron_variant, non_coding_transcript_variant
CT69	NR_125852.1	n.934+2037A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CT69	ENST00000417483.5	n.316+2037A>G		intron_variant, non_coding_transcript_variant		3
LINC01010	ENST00000431422.3	n.621-12325T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.691

Alfa AF: 0.716 Hom.: 41505

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321453; hg19: chr6-134773554;