chr6-134411396-T-G

Variant names:

• chr6-134411396-T-G
• rs9493942
• ENST00000431422.3:n.54-25919T>G

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-25919T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,144 control chromosomes in the GnomAD database, including 14,778 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 0.34 (14778 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01010	ENST00000431422.3	TSL:2	n.54-25919T>G		intron	N/A
	LINC01010	ENST00000660399.1		n.54-53345T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51911 AN: 152026 Hom.: 14730 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.342 AC: 52001 AN: 152144 Hom.: 14778 Cov.: 32 AF XY: 0.333 AC XY: 24749 AN XY: 74382

African (AFR) AF: 0.781 AC: 32390 AN: 41470

American (AMR) AF: 0.224 AC: 3418 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3472

East Asian (EAS) AF: 0.158 AC: 818 AN: 5176

South Asian (SAS) AF: 0.176 AC: 848 AN: 4826

European-Finnish (FIN) AF: 0.102 AC: 1085 AN: 10602

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11100 AN: 67994

Other (OTH) AF: 0.347 AC: 732 AN: 2112

Alfa AF: 0.236 Hom.: 7562

Bravo AF: 0.372

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.52
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs9493942; hg19: chr6-134732534;