chr6-134407056-T-A

Variant names:

• chr6-134407056-T-A
• rs9321439
• ENST00000431422.3:n.54-30259T>A

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-30259T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,142 control chromosomes in the GnomAD database, including 15,116 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 (15116 hom., cov: 33)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01010	ENST00000431422.3	TSL:2	n.54-30259T>A		intron	N/A
	LINC01010	ENST00000660399.1		n.54-57685T>A		intron	N/A
	LINC01010	ENST00000792709.1		n.*13T>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52848 AN: 152024 Hom.: 15066 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.348 AC: 52940 AN: 152142 Hom.: 15116 Cov.: 33 AF XY: 0.339 AC XY: 25190 AN XY: 74386

African (AFR) AF: 0.788 AC: 32706 AN: 41494

American (AMR) AF: 0.231 AC: 3533 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3472

East Asian (EAS) AF: 0.158 AC: 819 AN: 5180

South Asian (SAS) AF: 0.178 AC: 858 AN: 4826

European-Finnish (FIN) AF: 0.104 AC: 1099 AN: 10592

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11562 AN: 67992

Other (OTH) AF: 0.354 AC: 748 AN: 2112

Alfa AF: 0.270 Hom.: 1219

Bravo AF: 0.378

Asia WGS AF: 0.199 AC: 693 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9321439; hg19: chr6-134728194;