rs1029541

Variant names:

• chr7-84509688-C-T
• rs1029541
• ENST00000446000.2:n.82+7154C>T

Variant summary

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

The ENST00000446000.2(LINC03017):​n.82+7154C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,924 control chromosomes in the GnomAD database, including 5,027 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 0.24 (5027 hom., cov: 32)
• Consequence: LINC03017 ENST00000446000.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 3 publications found

Genes affected

LINC03017 (HGNC:56146): (long intergenic non-protein coding RNA 3017)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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
LINC03017	ENST00000446000.2	n.82+7154C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.244 AC: 36980 AN: 151806 Hom.: 5021 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.244 AC: 37021 AN: 151924 Hom.: 5027 Cov.: 32 AF XY: 0.238 AC XY: 17659 AN XY: 74242

African (AFR) AF: 0.365 AC: 15123 AN: 41418

American (AMR) AF: 0.186 AC: 2836 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3464

East Asian (EAS) AF: 0.156 AC: 801 AN: 5132

South Asian (SAS) AF: 0.116 AC: 559 AN: 4820

European-Finnish (FIN) AF: 0.133 AC: 1409 AN: 10586

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14722 AN: 67946

Other (OTH) AF: 0.255 AC: 538 AN: 2112

Alfa AF: 0.224 Hom.: 6559

Bravo AF: 0.252

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1029541; hg19: chr7-84139004;