rs6907728

chr6-131907629-A-Cchr6-131907629-A-G

Variant summary

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

The ENST00000421310.6(LINC01013):n.601+99A>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 0.165 in 151,954 control chromosomes in the GnomAD database, including 2,845 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 0.17 (2844 hom., cov: 32)
  • Exomes 𝑓: 0.14 (1 hom.)
• Consequence: LINC01013 ENST00000421310.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

Genes affected

LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)

ACMG classification

Verdict is Benign. Variant got -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 = 0.305 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
LINC01013	ENST00000421310.6	n.601+99A>C		intron_variant, non_coding_transcript_variant		5
LINC01013	ENST00000454596.2	n.189+5478A>C		intron_variant, non_coding_transcript_variant		2
LINC01013	ENST00000706294.1	n.182+5478A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25032 AN: 151790 Hom.: 2835 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.143 AC: 6 AN: 42 Hom.: 1 AF XY: 0.147 AC XY: 5 AN XY: 34

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.118

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.165 AC: 25085 AN: 151912 Hom.: 2844 Cov.: 32 AF XY: 0.162 AC XY: 12070 AN XY: 74278

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.0858

Gnomad4 FIN AF: 0.0663

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.163

Alfa AF: 0.111 Hom.: 1923

Bravo AF: 0.181

Asia WGS AF: 0.190 AC: 660 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	3.9
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6907728; hg19: chr6-132228769;