rs12100904

Variant names:

• chr14-36015774-A-G
• rs12100904
• ENST00000550089.2:n.463+17190A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-36015774-A-G
• chr14-36015774-A-T

Variant summary

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

The ENST00000550089.2(LINC00609):​n.463+17190A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,960 control chromosomes in the GnomAD database, including 14,897 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 0.43 (14897 hom., cov: 32)
• Consequence: LINC00609 ENST00000550089.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 2 publications found

Genes affected

LINC00609 (HGNC:43960): (long intergenic non-protein coding RNA 609)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550089.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00609	ENST00000550089.2	TSL:3	n.463+17190A>G		intron	N/A
	LINC00609	ENST00000660969.2		n.515+17190A>G		intron	N/A
	LINC00609	ENST00000662718.2		n.351+17190A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65984 AN: 151842 Hom.: 14877 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.435 AC: 66047 AN: 151960 Hom.: 14897 Cov.: 32 AF XY: 0.439 AC XY: 32610 AN XY: 74246

African (AFR) AF: 0.497 AC: 20594 AN: 41456

American (AMR) AF: 0.532 AC: 8129 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3138 AN: 5142

South Asian (SAS) AF: 0.498 AC: 2393 AN: 4808

European-Finnish (FIN) AF: 0.398 AC: 4198 AN: 10552

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24639 AN: 67954

Other (OTH) AF: 0.440 AC: 926 AN: 2106

Alfa AF: 0.413 Hom.: 4443

Bravo AF: 0.445

Asia WGS AF: 0.533 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.50
PhyloP100		1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12100904;

hg19: chr14-36484980;