rs1859849

Variant names:

• chr7-25679184-T-C
• rs1859849
• ENST00000456777.7:n.253-17453A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000456777.7(LINC03007):​n.253-17453A>G variant causes a intron 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 ENST00000456777.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

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

ENSG00000286725 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC03007	NR_157808.1	n.368-17453A>G		intron_variant	Intron 1 of 4
LINC03007	NR_157809.1	n.93-17453A>G		intron_variant	Intron 1 of 4
LINC03007	NR_157810.1	n.93-17453A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03007	ENST00000456777.7	n.253-17453A>G		intron_variant	Intron 1 of 3	3
LINC03007	ENST00000659634.1	n.248-17453A>G		intron_variant	Intron 1 of 4
LINC03007	ENST00000671106.2	n.200-17453A>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.250 AC: 10381 AN: 41480

American (AMR) AF: 0.317 AC: 4840 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3235 AN: 5128

South Asian (SAS) AF: 0.362 AC: 1739 AN: 4800

European-Finnish (FIN) AF: 0.241 AC: 2553 AN: 10572

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16032 AN: 67966

Other (OTH) AF: 0.254 AC: 538 AN: 2114

Alfa AF: 0.250 Hom.: 620

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
PhyloP100		-1.5

Splicing

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

Publications

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Other links and lift over

dbSNP: rs1859849; hg19: chr7-25718804;