6-134412590-A-C

Position:

• chr6-134412590-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431422.3(LINC01010):​n.54-24725A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,148 control chromosomes in the GnomAD database, including 12,912 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 0.32 (12912 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01010	ENST00000431422.3	n.54-24725A>C		intron_variant, non_coding_transcript_variant		2
LINC01010	ENST00000660399.1	n.54-52151A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49343 AN: 152030 Hom.: 12881 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.325 AC: 49413 AN: 152148 Hom.: 12912 Cov.: 32 AF XY: 0.316 AC XY: 23518 AN XY: 74402

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.331

Alfa AF: 0.222 Hom.: 3439

Bravo AF: 0.352

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2327484; hg19: chr6-134733728;