7-25660241-A-G

Position:

• chr7-25660241-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_157808.1(LINC03007):​n.429+1429T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 151,846 control chromosomes in the GnomAD database, including 46,853 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 0.78 (46853 hom., cov: 29)
• Consequence: LINC03007 NR_157808.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03007	NR_157808.1	n.429+1429T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03007	ENST00000456777.6	n.309+1429T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118422 AN: 151728 Hom.: 46797 Cov.: 29

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.781 AC: 118543 AN: 151846 Hom.: 46853 Cov.: 29 AF XY: 0.777 AC XY: 57687 AN XY: 74220

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.779

Alfa AF: 0.792 Hom.: 8607

Bravo AF: 0.783

Asia WGS AF: 0.578 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.9
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs87; hg19: chr7-25699861;