rs1243400

Variant names:

• chr10-8934695-A-G
• rs1243400
• ENST00000837048.1:n.849+4331A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-8934695-A-G
• chr10-8934695-A-T

Variant summary

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

The ENST00000837048.1(LINC02676):​n.849+4331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,016 control chromosomes in the GnomAD database, including 10,922 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 0.37 (10922 hom., cov: 32)
• Consequence: LINC02676 ENST00000837048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 7 publications found

Genes affected

LINC02676 (HGNC:54170): (long intergenic non-protein coding RNA 2676)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 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
LINC02676	ENST00000837048.1	n.849+4331A>G		intron_variant	Intron 2 of 4
LINC02676	ENST00000837049.1	n.716-9403A>G		intron_variant	Intron 1 of 4
LINC02676	ENST00000837050.1	n.704-31848A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56047 AN: 151896 Hom.: 10904 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.369 AC: 56097 AN: 152016 Hom.: 10922 Cov.: 32 AF XY: 0.368 AC XY: 27349 AN XY: 74286

African (AFR) AF: 0.365 AC: 15119 AN: 41448

American (AMR) AF: 0.463 AC: 7075 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1222 AN: 3466

East Asian (EAS) AF: 0.671 AC: 3456 AN: 5154

South Asian (SAS) AF: 0.464 AC: 2239 AN: 4824

European-Finnish (FIN) AF: 0.232 AC: 2446 AN: 10558

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.343 AC: 23341 AN: 67978

Other (OTH) AF: 0.409 AC: 864 AN: 2110

Alfa AF: 0.355 Hom.: 7797

Bravo AF: 0.390

Asia WGS AF: 0.555 AC: 1929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs1243400; hg19: chr10-8976658;