rs87

Variant names:

• chr7-25660241-A-G
• rs87
• ENST00000661881.2:n.1886T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-25660241-A-G
• chr7-25660241-A-T

Variant summary

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

The ENST00000661881.2(LINC03007):​n.1886T>C variant causes a non coding transcript exon 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 ENST00000661881.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 0 publications found

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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661881.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03007	NR_157808.1		n.429+1429T>C		intron	N/A
	LINC03007	NR_157809.1		n.154+1429T>C		intron	N/A
	LINC03007	NR_157810.1		n.154+1429T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03007	ENST00000661881.2		n.1886T>C		non_coding_transcript_exon	Exon 2 of 2
	LINC03007	ENST00000671106.2		n.1690T>C		non_coding_transcript_exon	Exon 2 of 2
	LINC03007	ENST00000423689.3	TSL:3	n.489+1429T>C		intron	N/A

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

African (AFR) AF: 0.828 AC: 34307 AN: 41412

American (AMR) AF: 0.807 AC: 12308 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2614 AN: 3472

East Asian (EAS) AF: 0.361 AC: 1861 AN: 5160

South Asian (SAS) AF: 0.638 AC: 3048 AN: 4776

European-Finnish (FIN) AF: 0.799 AC: 8433 AN: 10554

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.786 AC: 53384 AN: 67914

Other (OTH) AF: 0.779 AC: 1638 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.9
DANN	Benign	0.88
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs87; hg19: chr7-25699861;