7-25574965-A-G

Variant names:

• chr7-25574965-A-G
• rs2813890
• ENST00000812180.1:n.624-5075T>C

Variant summary

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

The ENST00000812180.1(LINC03007):​n.624-5075T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,088 control chromosomes in the GnomAD database, including 27,299 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 0.60 (27299 hom., cov: 33)
• Consequence: LINC03007 ENST00000812180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 1 publications found

Genes affected

LINC03007 (HGNC:56132): (long intergenic non-protein coding RNA 3007)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 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
LINC03007	ENST00000812180.1	n.624-5075T>C		intron_variant	Intron 4 of 4
LINC03007	ENST00000812191.1	n.608-5075T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90511 AN: 151968 Hom.: 27280 Cov.: 33

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.596 AC: 90583 AN: 152088 Hom.: 27299 Cov.: 33 AF XY: 0.595 AC XY: 44240 AN XY: 74354

African (AFR) AF: 0.619 AC: 25695 AN: 41508

American (AMR) AF: 0.671 AC: 10259 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2255 AN: 3470

East Asian (EAS) AF: 0.802 AC: 4153 AN: 5180

South Asian (SAS) AF: 0.577 AC: 2783 AN: 4822

European-Finnish (FIN) AF: 0.527 AC: 5548 AN: 10534

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 38008 AN: 67978

Other (OTH) AF: 0.608 AC: 1286 AN: 2114

Alfa AF: 0.576 Hom.: 3324

Bravo AF: 0.611

Asia WGS AF: 0.660 AC: 2294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	13
DANN	Benign	0.60
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs2813890; hg19: chr7-25614585;