chr7-76580142-A-G

Variant names:

• chr7-76580142-A-G
• rs17718122
• ENST00000418663.5:n.605+28620A>G

Variant summary

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

The ENST00000418663.5(LINC03009):​n.605+28620A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,624 control chromosomes in the GnomAD database, including 5,279 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 0.25 (5279 hom., cov: 31)
• Consequence: LINC03009 ENST00000418663.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 30 publications found

Genes affected

LINC03009 (HGNC:56134): (long intergenic non-protein coding RNA 3009)

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 (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418663.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03009	NR_029411.1		n.624+28620A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03009	ENST00000418663.5	TSL:1	n.605+28620A>G		intron	N/A
	LINC03009	ENST00000450661.1	TSL:1	n.604+28620A>G		intron	N/A
	LINC03009	ENST00000423084.1	TSL:3	n.305+28620A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37857 AN: 151504 Hom.: 5273 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.250 AC: 37862 AN: 151624 Hom.: 5279 Cov.: 31 AF XY: 0.244 AC XY: 18102 AN XY: 74124

African (AFR) AF: 0.173 AC: 7164 AN: 41390

American (AMR) AF: 0.218 AC: 3321 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1079 AN: 3452

East Asian (EAS) AF: 0.0491 AC: 253 AN: 5150

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2147 AN: 10582

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21663 AN: 67728

Other (OTH) AF: 0.292 AC: 612 AN: 2098

Alfa AF: 0.287 Hom.: 16755

Bravo AF: 0.249

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.61
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs17718122; hg19: chr7-76209459;