rs729739

Variant names:

• chr10-62670542-G-A
• rs729739
• ENST00000395251.5:n.1226G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000395251.5(LINC02929):​n.1226G>A variant causes a non coding transcript exon 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: LINC02929 ENST00000395251.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723
• Publications: 12 publications found

Genes affected

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

ENSG00000285837 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000395251.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02929	ENST00000395251.5	TSL:1	n.1226G>A		non_coding_transcript_exon	Exon 7 of 7
	ENSG00000285837	ENST00000647733.1		c.*241G>A		3_prime_UTR	Exon 8 of 8	ENSP00000502188.1
	LINC02929	ENST00000344640.7	TSL:1	n.*168G>A		downstream_gene	N/A

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

African (AFR) AF: 0.0601 AC: 422 AN: 7016

American (AMR) AF: 0.175 AC: 1706 AN: 9764

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 1919 AN: 6696

East Asian (EAS) AF: 0.105 AC: 1656 AN: 15802

South Asian (SAS) AF: 0.156 AC: 2426 AN: 15542

European-Finnish (FIN) AF: 0.235 AC: 2656 AN: 11294

Middle Eastern (MID) AF: 0.272 AC: 244 AN: 896

European-Non Finnish (NFE) AF: 0.265 AC: 30911 AN: 116452

Other (OTH) AF: 0.233 AC: 2813 AN: 12092

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

African (AFR) AF: 0.0498 AC: 2063 AN: 41426

American (AMR) AF: 0.186 AC: 2840 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3468

East Asian (EAS) AF: 0.0950 AC: 491 AN: 5170

South Asian (SAS) AF: 0.136 AC: 654 AN: 4822

European-Finnish (FIN) AF: 0.248 AC: 2619 AN: 10572

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17689 AN: 67980

Other (OTH) AF: 0.217 AC: 457 AN: 2108

Alfa AF: 0.219 Hom.: 2158

Bravo AF: 0.175

Asia WGS AF: 0.145 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.25
PhyloP100		0.72
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs729739; hg19: chr10-64430302;