chr7-25581959-G-T

Variant names:

• chr7-25581959-G-T
• rs208549
• ENST00000812180.1:n.624-12069C>A

Variant summary

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

The ENST00000812180.1(LINC03007):​n.624-12069C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,008 control chromosomes in the GnomAD database, including 37,137 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 0.69 (37137 hom., cov: 31)
• Consequence: LINC03007 ENST00000812180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 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.624-12069C>A		intron_variant	Intron 4 of 4
LINC03007	ENST00000812191.1	n.608-12069C>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105438 AN: 151890 Hom.: 37097 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.694 AC: 105543 AN: 152008 Hom.: 37137 Cov.: 31 AF XY: 0.692 AC XY: 51440 AN XY: 74282

African (AFR) AF: 0.772 AC: 32027 AN: 41470

American (AMR) AF: 0.751 AC: 11476 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2506 AN: 3464

East Asian (EAS) AF: 0.850 AC: 4369 AN: 5142

South Asian (SAS) AF: 0.713 AC: 3439 AN: 4822

European-Finnish (FIN) AF: 0.568 AC: 5992 AN: 10546

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43591 AN: 67974

Other (OTH) AF: 0.703 AC: 1481 AN: 2108

Alfa AF: 0.658 Hom.: 122900

Bravo AF: 0.711

Asia WGS AF: 0.790 AC: 2744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.46
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs208549; hg19: chr7-25621579;