rs3123712

Variant names:

• chr10-43024243-A-G
• rs3123712
• ENST00000754421.1:n.440+1698T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-43024243-A-G
• chr10-43024243-A-T

Variant summary

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

The ENST00000754421.1(LINC01264):​n.440+1698T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0676 in 152,306 control chromosomes in the GnomAD database, including 472 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 0.068 (472 hom., cov: 33)
• Consequence: LINC01264 ENST00000754421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 1 publications found

Genes affected

LINC01264 (HGNC:50282): (long intergenic non-protein coding RNA 1264)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0971 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
LINC01264	ENST00000754421.1	n.440+1698T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0677 AC: 10307 AN: 152188 Hom.: 472 Cov.: 33

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0848

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.0676 AC: 10300 AN: 152306 Hom.: 472 Cov.: 33 AF XY: 0.0653 AC XY: 4865 AN XY: 74486

African (AFR) AF: 0.0251 AC: 1045 AN: 41570

American (AMR) AF: 0.0641 AC: 980 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0848 AC: 294 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0391 AC: 189 AN: 4834

European-Finnish (FIN) AF: 0.0771 AC: 819 AN: 10620

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0991 AC: 6739 AN: 68008

Other (OTH) AF: 0.0723 AC: 153 AN: 2116

Alfa AF: 0.0781 Hom.: 72

Bravo AF: 0.0646

Asia WGS AF: 0.0220 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.91
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs3123712; hg19: chr10-43519691;