7-25573041-G-A

Variant names:

• chr7-25573041-G-A
• rs975369
• ENST00000812180.1:n.624-3151C>T

Variant summary

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

The ENST00000812180.1(LINC03007):​n.624-3151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0941 in 152,240 control chromosomes in the GnomAD database, including 1,015 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 0.094 (1015 hom., cov: 32)
• Consequence: LINC03007 ENST00000812180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812180.1. 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
	LINC03007	ENST00000812180.1		n.624-3151C>T		intron	N/A
	LINC03007	ENST00000812191.1		n.608-3151C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0940 AC: 14307 AN: 152124 Hom.: 1016 Cov.: 32

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0996

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.0941 AC: 14326 AN: 152240 Hom.: 1015 Cov.: 32 AF XY: 0.0995 AC XY: 7404 AN XY: 74430

African (AFR) AF: 0.0854 AC: 3550 AN: 41546

American (AMR) AF: 0.0997 AC: 1525 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3470

East Asian (EAS) AF: 0.432 AC: 2233 AN: 5166

South Asian (SAS) AF: 0.179 AC: 860 AN: 4816

European-Finnish (FIN) AF: 0.0876 AC: 929 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0667 AC: 4536 AN: 68022

Other (OTH) AF: 0.0918 AC: 194 AN: 2114

Alfa AF: 0.0774 Hom.: 925

Bravo AF: 0.0957

Asia WGS AF: 0.261 AC: 905 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.19
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs975369; hg19: chr7-25612661;