rs7745875

Positions:

• chr6-132096424-G-A

Variant summary

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

The ENST00000706336.1(LINC01013):​n.155-72577G>A 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 0.0964 in 152,066 control chromosomes in the GnomAD database, including 983 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 0.096 (983 hom., cov: 32)
• Consequence: LINC01013 ENST00000706336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 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	ENST00000706336.1	n.155-72577G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14642 AN: 151948 Hom.: 980 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.00598

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0964 AC: 14654 AN: 152066 Hom.: 983 Cov.: 32 AF XY: 0.0932 AC XY: 6925 AN XY: 74340

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.00599

Gnomad4 SAS AF: 0.0380

Gnomad4 FIN AF: 0.0463

Gnomad4 NFE AF: 0.0705

Gnomad4 OTH AF: 0.0803

Alfa AF: 0.0732 Hom.: 188

Bravo AF: 0.102

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7745875; hg19: chr6-132417564;