rs1859849

Positions:

• chr7-25679184-T-C
• chr7-25679184-T-G

Variant summary

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

The NR_157808.1(LINC03007):​n.368-17453A>G 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 0.268 in 152,014 control chromosomes in the GnomAD database, including 5,876 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 0.27 (5876 hom., cov: 32)
• Consequence: LINC03007 NR_157808.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03007	NR_157808.1	n.368-17453A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03007	ENST00000456777.6	n.248-17453A>G		intron_variant, non_coding_transcript_variant		3
LINC03007	ENST00000659634.1	n.248-17453A>G		intron_variant, non_coding_transcript_variant
LINC03007	ENST00000671106.1	n.125-17453A>G		intron_variant, non_coding_transcript_variant
LINC03007	ENST00000702191.1	n.194-17453A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40735 AN: 151896 Hom.: 5874 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.268 AC: 40756 AN: 152014 Hom.: 5876 Cov.: 32 AF XY: 0.273 AC XY: 20269 AN XY: 74316

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.254

Alfa AF: 0.249 Hom.: 589

Bravo AF: 0.273

Asia WGS AF: 0.437 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1859849; hg19: chr7-25718804;