rs10588631

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000511291.1(ENSG00000251216):​n.146-29287G>T variant causes a intron, non coding transcript 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: ENST00000511291.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.13

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377544	XR_939482.3	n.291+1228C>A		intron_variant, non_coding_transcript_variant
LOC105377543	XR_001741463.1	n.270-19914G>T		intron_variant, non_coding_transcript_variant
LOC105377543	XR_939480.2	n.270-19914G>T		intron_variant, non_coding_transcript_variant
LOC105377544	XR_939483.3	n.223+1228C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000511291.1	n.146-29287G>T		intron_variant, non_coding_transcript_variant		3
LINC02269	ENST00000656853.1	n.641+1228C>A		intron_variant, non_coding_transcript_variant
	ENST00000662648.1	n.423-19914G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.425

Alfa AF: 0.417 Hom.: 1118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10588631; hg19: chr4-174878428;