rs10588631

Variant names:

• chr4-173957277-C-A
• rs10588631
• ENST00000511291.1:n.146-29287G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-173957277-C-A
• chr4-173957277-C-G
• chr4-173957277-C-T

Variant summary

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

The ENST00000511291.1(ENSG00000251216):​n.146-29287G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 132,264 control chromosomes in the GnomAD database, including 10,269 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 0.41 (10269 hom., cov: 21)
• Consequence: ENSG00000251216 ENST00000511291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.13
• Publications: 0 publications found

Genes affected

ENSG00000251216 (HGNC:):

LINC02269 (HGNC:53184): (long intergenic non-protein coding RNA 2269)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511291.1. 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
	LOC105377543	NR_188466.1		n.365-19914G>T		intron	N/A
	LOC105377543	NR_188467.1		n.261-19914G>T		intron	N/A
	LOC105377543	NR_188468.1		n.261-19914G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251216	ENST00000511291.1	TSL:3	n.146-29287G>T		intron	N/A
	LINC02269	ENST00000656853.1		n.641+1228C>A		intron	N/A
	ENSG00000251216	ENST00000662648.2		n.423-19914G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.413 AC: 54670 AN: 132214 Hom.: 10271 Cov.: 21

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.413 AC: 54683 AN: 132264 Hom.: 10269 Cov.: 21 AF XY: 0.410 AC XY: 26377 AN XY: 64276

African (AFR) AF: 0.408 AC: 13063 AN: 32052

American (AMR) AF: 0.403 AC: 5288 AN: 13108

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1543 AN: 3252

East Asian (EAS) AF: 0.354 AC: 1634 AN: 4618

South Asian (SAS) AF: 0.321 AC: 1211 AN: 3768

European-Finnish (FIN) AF: 0.351 AC: 3071 AN: 8746

Middle Eastern (MID) AF: 0.390 AC: 110 AN: 282

European-Non Finnish (NFE) AF: 0.434 AC: 27664 AN: 63768

Other (OTH) AF: 0.425 AC: 798 AN: 1876

Alfa AF: 0.417 Hom.: 1118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0020
DANN	Benign	0.097
PhyloP100		-7.1

Splicing

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

Other links and lift over

dbSNP: rs10588631; hg19: chr4-174878428;