rs17645907

Variant names:

• chr7-76659716-T-C
• rs17645907
• ENST00000740690.1:n.153-29412T>C

Variant summary

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

The ENST00000740690.1(LINC03009):​n.153-29412T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,934 control chromosomes in the GnomAD database, including 5,234 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 0.26 (5234 hom., cov: 32)
• Consequence: LINC03009 ENST00000740690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 8 publications found

Genes affected

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

ENSG00000296620 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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
LINC03009	ENST00000740690.1	n.153-29412T>C		intron_variant	Intron 2 of 2
LINC03009	ENST00000740691.1	n.249-29412T>C		intron_variant	Intron 2 of 2
ENSG00000296620	ENST00000740833.1	n.507-8834A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39670 AN: 151818 Hom.: 5229 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0167

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.261 AC: 39706 AN: 151934 Hom.: 5234 Cov.: 32 AF XY: 0.260 AC XY: 19330 AN XY: 74280

African (AFR) AF: 0.302 AC: 12501 AN: 41382

American (AMR) AF: 0.263 AC: 4016 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3464

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5190

South Asian (SAS) AF: 0.242 AC: 1170 AN: 4830

European-Finnish (FIN) AF: 0.225 AC: 2384 AN: 10578

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17652 AN: 67926

Other (OTH) AF: 0.270 AC: 570 AN: 2108

Alfa AF: 0.261 Hom.: 17050

Bravo AF: 0.262

Asia WGS AF: 0.130 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.5
DANN	Benign	0.42
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs17645907; hg19: chr7-76289033;