rs6922545

chr6-134407836-T-C

Variant summary

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

The ENST00000431422.3(LINC01010):n.54-29479T>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 0.346 in 152,106 control chromosomes in the GnomAD database, including 14,868 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 0.35 (14868 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

Genes affected

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01010	ENST00000431422.3	n.54-29479T>C		intron_variant, non_coding_transcript_variant		2
LINC01010	ENST00000660399.1	n.54-56905T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52536 AN: 151988 Hom.: 14822 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.346 AC: 52624 AN: 152106 Hom.: 14868 Cov.: 32 AF XY: 0.337 AC XY: 25033 AN XY: 74366

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.353

Alfa AF: 0.261 Hom.: 1508

Bravo AF: 0.376

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.52
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6922545; hg19: chr6-134728974;