rs4255618

Variant names:

• chr12-131352932-A-C
• rs4255618
• ENST00000659569.1:n.496T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-131352932-A-C
• chr12-131352932-A-G
• chr12-131352932-A-T

Variant summary

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

The ENST00000659569.1(ENSG00000287792):​n.496T>G 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 0.356 in 151,906 control chromosomes in the GnomAD database, including 9,754 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 0.36 (9754 hom., cov: 34)
• Consequence: ENSG00000287792 ENST00000659569.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 1 publications found

Genes affected

ENSG00000287792 (HGNC:):

LINC02370 (HGNC:27885): (long intergenic non-protein coding RNA 2370)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02370	NR_103736.1	n.409+3388A>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287792	ENST00000659569.1	n.496T>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02370	ENST00000428272.4	n.409+3388A>C		intron_variant	Intron 2 of 2	5
LINC02370	ENST00000743505.1	n.1164+5271A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54031 AN: 151788 Hom.: 9747 Cov.: 34

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.356 AC: 54055 AN: 151906 Hom.: 9754 Cov.: 34 AF XY: 0.355 AC XY: 26384 AN XY: 74282

African (AFR) AF: 0.358 AC: 14827 AN: 41390

American (AMR) AF: 0.367 AC: 5613 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1775 AN: 3458

East Asian (EAS) AF: 0.426 AC: 2191 AN: 5146

South Asian (SAS) AF: 0.372 AC: 1793 AN: 4822

European-Finnish (FIN) AF: 0.248 AC: 2620 AN: 10568

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23842 AN: 67932

Other (OTH) AF: 0.377 AC: 797 AN: 2112

Alfa AF: 0.335 Hom.: 1238

Bravo AF: 0.366

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	2.4
DANN	Benign	0.40
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs4255618; hg19: chr12-131837477;