rs1754162

Variant names:

• chr7-76633461-T-C
• rs1754162
• ENST00000740690.1:n.153-55667T>C

Variant summary

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

The ENST00000740690.1(LINC03009):​n.153-55667T>C variant causes a intron change. 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 (3339 hom., cov: 19)
• Consequence: LINC03009 ENST00000740690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 0 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740690.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03009	ENST00000740690.1		n.153-55667T>C		intron	N/A
	LINC03009	ENST00000740691.1		n.249-55667T>C		intron	N/A
	LINC03009	ENST00000740692.1		n.408-16980T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 21634 AN: 130290 Hom.: 3333 Cov.: 19

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.273

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.166 AC: 21645 AN: 130390 Hom.: 3339 Cov.: 19 AF XY: 0.163 AC XY: 10251 AN XY: 62932

African (AFR) AF: 0.0906 AC: 3464 AN: 38214

American (AMR) AF: 0.152 AC: 1895 AN: 12440

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 698 AN: 2844

East Asian (EAS) AF: 0.0464 AC: 201 AN: 4332

South Asian (SAS) AF: 0.184 AC: 632 AN: 3440

European-Finnish (FIN) AF: 0.126 AC: 1113 AN: 8806

Middle Eastern (MID) AF: 0.289 AC: 74 AN: 256

European-Non Finnish (NFE) AF: 0.226 AC: 13004 AN: 57538

Other (OTH) AF: 0.195 AC: 340 AN: 1748

Alfa AF: 0.202 Hom.: 670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.7
DANN	Benign	0.51

Splicing

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

Other links and lift over

dbSNP: rs1754162; hg19: chr7-76262778;