rs1076782

Variant names:

• chr6-134411741-G-A
• rs1076782
• ENST00000431422.3:n.54-25574G>A

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-25574G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 1 publications found

Genes affected

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431422.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01010	ENST00000431422.3	TSL:2	n.54-25574G>A		intron	N/A
	LINC01010	ENST00000660399.1		n.54-53000G>A		intron	N/A

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

African (AFR) AF: 0.522 AC: 21600 AN: 41404

American (AMR) AF: 0.0918 AC: 1404 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5174

South Asian (SAS) AF: 0.0900 AC: 434 AN: 4824

European-Finnish (FIN) AF: 0.00575 AC: 61 AN: 10612

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0290 AC: 1969 AN: 68008

Other (OTH) AF: 0.159 AC: 336 AN: 2110

Alfa AF: 0.0660 Hom.: 2534

Bravo AF: 0.196

Asia WGS AF: 0.0670 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		-0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1076782;

hg19: chr6-134732879;