rs729739

Positions:

• chr10-62670542-G-A
• chr10-62670542-G-T

Variant summary

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

The XM_047426120.1(LOC124902436):​c.*241G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 347,590 control chromosomes in the GnomAD database, including 8,912 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 0.19 (3352 hom., cov: 32)
  • Exomes 𝑓: 0.23 (5560 hom.)
• Consequence: LOC124902436 XM_047426120.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723

Genes affected

LOC124902436 (HGNC:):

LINC02929 (HGNC:55812): (long intergenic non-protein coding RNA 2929)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902436	XM_047426120.1	c.*241G>A		3_prime_UTR_variant	6/6
LOC124902436	XM_047426118.1	c.*241G>A		3_prime_UTR_variant	6/6
LOC124902436	XM_047426121.1	c.*241G>A		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02929	ENST00000395251.5	n.1226G>A		non_coding_transcript_exon_variant	7/7	1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28247 AN: 151918 Hom.: 3348 Cov.: 32

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0957

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.229 AC: 44753 AN: 195554 Hom.: 5560 Cov.: 0 AF XY: 0.227 AC XY: 22912 AN XY: 100906

Gnomad4 AFR exome AF: 0.0601

Gnomad4 AMR exome AF: 0.175

Gnomad4 ASJ exome AF: 0.287

Gnomad4 EAS exome AF: 0.105

Gnomad4 SAS exome AF: 0.156

Gnomad4 FIN exome AF: 0.235

Gnomad4 NFE exome AF: 0.265

Gnomad4 OTH exome AF: 0.233

GnomAD4 genome AF: 0.186 AC: 28247 AN: 152036 Hom.: 3352 Cov.: 32 AF XY: 0.185 AC XY: 13741 AN XY: 74326

Gnomad4 AFR AF: 0.0498

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.0950

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.217

Alfa AF: 0.219 Hom.: 1881

Bravo AF: 0.175

Asia WGS AF: 0.145 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs729739; hg19: chr10-64430302;