rs2787423

Variant names:

• chr14-36217848-G-A
• rs2787423
• ENST00000556542.2:n.2001+2333G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-36217848-G-A
• chr14-36217848-G-C

Variant summary

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

The ENST00000556542.2(LINC00609):​n.2001+2333G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,036 control chromosomes in the GnomAD database, including 6,814 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 0.30 (6814 hom., cov: 32)
• Consequence: LINC00609 ENST00000556542.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00609	ENST00000556542.2	n.2001+2333G>A		intron_variant	Intron 2 of 2	4
LINC00609	ENST00000818312.1	n.835-17476G>A		intron_variant	Intron 6 of 6
LINC00609	ENST00000818313.1	n.1486+2333G>A		intron_variant	Intron 9 of 9
LINC00609	ENST00000818336.1	n.68+2333G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44932 AN: 151918 Hom.: 6802 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.296 AC: 44967 AN: 152036 Hom.: 6814 Cov.: 32 AF XY: 0.296 AC XY: 22016 AN XY: 74292

African (AFR) AF: 0.231 AC: 9595 AN: 41472

American (AMR) AF: 0.298 AC: 4550 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1253 AN: 3472

East Asian (EAS) AF: 0.380 AC: 1954 AN: 5146

South Asian (SAS) AF: 0.459 AC: 2206 AN: 4808

European-Finnish (FIN) AF: 0.263 AC: 2786 AN: 10582

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21541 AN: 67972

Other (OTH) AF: 0.324 AC: 684 AN: 2114

Alfa AF: 0.306 Hom.: 3632

Bravo AF: 0.293

Asia WGS AF: 0.425 AC: 1478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	14
DANN	Benign	0.57
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs2787423; hg19: chr14-36687054;