rs1076782

Positions:

• chr6-134411741-G-A

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-25574G>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 0.172 in 152,100 control chromosomes in the GnomAD database, including 5,891 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 0.17 (5891 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01010	ENST00000431422.3	n.54-25574G>A		intron_variant, non_coding_transcript_variant		2
LINC01010	ENST00000660399.1	n.54-53000G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26147 AN: 151982 Hom.: 5877 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.00575

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.172 AC: 26209 AN: 152100 Hom.: 5891 Cov.: 32 AF XY: 0.168 AC XY: 12503 AN XY: 74378

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0900

Gnomad4 FIN AF: 0.00575

Gnomad4 NFE AF: 0.0290

Gnomad4 OTH AF: 0.159

Alfa AF: 0.112 Hom.: 1110

Bravo AF: 0.196

Asia WGS AF: 0.0670 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1076782; hg19: chr6-134732879;