12-47834985-A-T

Variant names:

• chr12-47834985-A-T
• rs11608702
• XR_007063291.1:n.1121A>T

Variant summary

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

The XR_007063291.1(LINC02354):​n.1121A>T 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 0.338 in 152,058 control chromosomes in the GnomAD database, including 9,402 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 0.34 (9402 hom., cov: 32)
• Consequence: LINC02354 XR_007063291.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 12 publications found

Genes affected

LINC02354 (HGNC:53276): (long intergenic non-protein coding RNA 2354)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548564.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02354	ENST00000548564.1	TSL:4	n.492+334A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51397 AN: 151942 Hom.: 9410 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.338 AC: 51399 AN: 152058 Hom.: 9402 Cov.: 32 AF XY: 0.341 AC XY: 25328 AN XY: 74324

African (AFR) AF: 0.247 AC: 10239 AN: 41486

American (AMR) AF: 0.387 AC: 5908 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3655 AN: 5164

South Asian (SAS) AF: 0.304 AC: 1465 AN: 4814

European-Finnish (FIN) AF: 0.361 AC: 3814 AN: 10570

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24327 AN: 67968

Other (OTH) AF: 0.344 AC: 725 AN: 2108

Alfa AF: 0.355 Hom.: 1228

Bravo AF: 0.342

Asia WGS AF: 0.477 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.73
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs11608702; hg19: chr12-48228768;