rs169642

Variant names:

• chr7-25584469-G-A
• rs169642
• ENST00000812180.1:n.623+10068C>T

Variant summary

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

The ENST00000812180.1(LINC03007):​n.623+10068C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,050 control chromosomes in the GnomAD database, including 28,267 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 0.61 (28267 hom., cov: 32)
• Consequence: LINC03007 ENST00000812180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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.623+10068C>T		intron_variant	Intron 4 of 4
LINC03007	ENST00000812191.1	n.607+10146C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92053 AN: 151932 Hom.: 28248 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.606 AC: 92130 AN: 152050 Hom.: 28267 Cov.: 32 AF XY: 0.605 AC XY: 45002 AN XY: 74344

African (AFR) AF: 0.651 AC: 27002 AN: 41458

American (AMR) AF: 0.676 AC: 10340 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2257 AN: 3468

East Asian (EAS) AF: 0.819 AC: 4235 AN: 5168

South Asian (SAS) AF: 0.598 AC: 2883 AN: 4818

European-Finnish (FIN) AF: 0.528 AC: 5582 AN: 10580

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37939 AN: 67962

Other (OTH) AF: 0.615 AC: 1297 AN: 2110

Alfa AF: 0.578 Hom.: 81826

Bravo AF: 0.621

Asia WGS AF: 0.690 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.88
DANN	Benign	0.41
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs169642; hg19: chr7-25624089;