rs7743107

chr6-134465324-T-Achr6-134465324-T-C

Variant summary

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

The NR_038216.1(LINC01010):n.484+266T>A 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 0.125 in 152,224 control chromosomes in the GnomAD database, including 2,819 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 0.13 (2819 hom., cov: 32)
• Consequence: LINC01010 NR_038216.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01010	NR_038216.1	n.484+266T>A		intron_variant, non_coding_transcript_variant
CT69	NR_125852.1	n.805+9792A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CT69	ENST00000417483.5	n.187+9792A>T		intron_variant, non_coding_transcript_variant		3
LINC01010	ENST00000431422.3	n.729+475T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19022 AN: 152106 Hom.: 2810 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.00302

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.125 AC: 19063 AN: 152224 Hom.: 2819 Cov.: 32 AF XY: 0.123 AC XY: 9172 AN XY: 74436

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0640

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.00302

Gnomad4 NFE AF: 0.0213

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0808 Hom.: 196

Bravo AF: 0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.6
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7743107; hg19: chr6-134786462;