chr6-134407424-A-C

Variant names:

• chr6-134407424-A-C
• rs9493934
• ENST00000431422.3:n.54-29891A>C

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-29891A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,114 control chromosomes in the GnomAD database, including 8,996 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 0.28 (8996 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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.54-29891A>C		intron	N/A
	LINC01010	ENST00000660399.1		n.54-57317A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43123 AN: 151994 Hom.: 8971 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.284 AC: 43188 AN: 152114 Hom.: 8996 Cov.: 32 AF XY: 0.277 AC XY: 20574 AN XY: 74376

African (AFR) AF: 0.591 AC: 24470 AN: 41434

American (AMR) AF: 0.192 AC: 2928 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3470

East Asian (EAS) AF: 0.158 AC: 821 AN: 5186

South Asian (SAS) AF: 0.175 AC: 845 AN: 4822

European-Finnish (FIN) AF: 0.101 AC: 1074 AN: 10598

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11064 AN: 68002

Other (OTH) AF: 0.281 AC: 595 AN: 2116

Alfa AF: 0.191 Hom.: 7909

Bravo AF: 0.307

Asia WGS AF: 0.186 AC: 646 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.49
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs9493934; hg19: chr6-134728562;