rs2503875

Variant names:

• chr10-43318601-G-A
• rs2503875
• ENST00000740938.1:n.113+6G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-43318601-G-A
• chr10-43318601-G-T

Variant summary

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

The ENST00000740938.1(LINC02633):​n.113+6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,162 control chromosomes in the GnomAD database, including 5,582 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 0.24 (5582 hom., cov: 32)
• Consequence: LINC02633 ENST00000740938.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 28 publications found

Genes affected

LINC02633 (HGNC:54116): (long intergenic non-protein coding RNA 2633)

LOC105378271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740938.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02633	ENST00000740938.1		n.113+6G>A		splice_region intron	N/A
	LINC02633	ENST00000740939.1		n.113+6G>A		splice_region intron	N/A
	LINC02633	ENST00000740940.1		n.137+6G>A		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37149 AN: 152044 Hom.: 5584 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.244 AC: 37148 AN: 152162 Hom.: 5582 Cov.: 32 AF XY: 0.248 AC XY: 18466 AN XY: 74390

African (AFR) AF: 0.0696 AC: 2890 AN: 41546

American (AMR) AF: 0.317 AC: 4841 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3466

East Asian (EAS) AF: 0.423 AC: 2190 AN: 5180

South Asian (SAS) AF: 0.384 AC: 1851 AN: 4820

European-Finnish (FIN) AF: 0.309 AC: 3267 AN: 10576

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20103 AN: 67978

Other (OTH) AF: 0.251 AC: 529 AN: 2108

Alfa AF: 0.281 Hom.: 22624

Bravo AF: 0.236

Asia WGS AF: 0.385 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.050
DANN	Benign	0.68
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2503875;

hg19: chr10-43814049;