chr6-134407836-T-C

Variant names:

• chr6-134407836-T-C
• rs6922545
• ENST00000431422.3:n.54-29479T>C

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-29479T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,106 control chromosomes in the GnomAD database, including 14,868 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 (14868 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01010	ENST00000431422.3	n.54-29479T>C		intron_variant	Intron 1 of 3	2
LINC01010	ENST00000660399.1	n.54-56905T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52536 AN: 151988 Hom.: 14822 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.346 AC: 52624 AN: 152106 Hom.: 14868 Cov.: 32 AF XY: 0.337 AC XY: 25033 AN XY: 74366

African (AFR) AF: 0.781 AC: 32391 AN: 41474

American (AMR) AF: 0.231 AC: 3529 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3470

East Asian (EAS) AF: 0.158 AC: 818 AN: 5172

South Asian (SAS) AF: 0.177 AC: 854 AN: 4820

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10600

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11565 AN: 67986

Other (OTH) AF: 0.353 AC: 744 AN: 2108

Alfa AF: 0.275 Hom.: 1731

Bravo AF: 0.376

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.37
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs6922545; hg19: chr6-134728974;