rs1346987

Variant names:

• chr18-42522676-C-A
• rs1346987
• ENST00000585639.5:n.682+6507C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-42522676-C-A
• chr18-42522676-C-G
• chr18-42522676-C-T

Variant summary

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

The ENST00000585639.5(LINC00907):​n.682+6507C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,922 control chromosomes in the GnomAD database, including 4,021 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 0.21 (4021 hom., cov: 32)
• Consequence: LINC00907 ENST00000585639.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 4 publications found

Genes affected

LINC00907 (HGNC:44327): (long intergenic non-protein coding RNA 907)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.873-52117C>A		intron_variant	Intron 6 of 9
LINC00907	NR_046454.1	n.703+6507C>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585639.5	n.682+6507C>A		intron_variant	Intron 6 of 6	1
LINC00907	ENST00000589068.5	n.838-52117C>A		intron_variant	Intron 6 of 9	2
LINC00907	ENST00000753323.1	n.556+67687C>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31375 AN: 151804 Hom.: 4010 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.207 AC: 31423 AN: 151922 Hom.: 4021 Cov.: 32 AF XY: 0.206 AC XY: 15312 AN XY: 74264

African (AFR) AF: 0.326 AC: 13498 AN: 41406

American (AMR) AF: 0.248 AC: 3783 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3470

East Asian (EAS) AF: 0.445 AC: 2285 AN: 5138

South Asian (SAS) AF: 0.0945 AC: 454 AN: 4806

European-Finnish (FIN) AF: 0.112 AC: 1182 AN: 10554

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.134 AC: 9077 AN: 67966

Other (OTH) AF: 0.202 AC: 425 AN: 2104

Alfa AF: 0.158 Hom.: 5424

Bravo AF: 0.227

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.58
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1346987; hg19: chr18-40102641;