chr7-76587304-C-T

Variant names:

• chr7-76587304-C-T
• rs11505688
• ENST00000418663.5:n.605+35782C>T

Variant summary

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

The ENST00000418663.5(LINC03009):​n.605+35782C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,032 control chromosomes in the GnomAD database, including 2,571 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 (2571 hom., cov: 31)
• Consequence: LINC03009 ENST00000418663.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 12 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=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 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+35782C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03009	ENST00000418663.5	TSL:1	n.605+35782C>T		intron	N/A
	LINC03009	ENST00000450661.1	TSL:1	n.604+35782C>T		intron	N/A
	LINC03009	ENST00000423084.1	TSL:3	n.306-28190C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26123 AN: 151916 Hom.: 2574 Cov.: 31

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.172 AC: 26132 AN: 152032 Hom.: 2571 Cov.: 31 AF XY: 0.171 AC XY: 12711 AN XY: 74308

African (AFR) AF: 0.0812 AC: 3370 AN: 41512

American (AMR) AF: 0.198 AC: 3028 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3462

East Asian (EAS) AF: 0.249 AC: 1283 AN: 5150

South Asian (SAS) AF: 0.268 AC: 1289 AN: 4806

European-Finnish (FIN) AF: 0.155 AC: 1636 AN: 10564

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14163 AN: 67960

Other (OTH) AF: 0.174 AC: 367 AN: 2108

Alfa AF: 0.124 Hom.: 271

Bravo AF: 0.172

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.71
DANN	Benign	0.91
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs11505688; hg19: chr7-76216621;