ENST00000647733.1:c.1129+15456C>T

Variant names:

• chr10-62638706-C-T
• rs10995251
• ENST00000647733.1:c.1129+15456C>T

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.1129+15456C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,096 control chromosomes in the GnomAD database, including 7,974 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 0.30 (7974 hom., cov: 31)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 40 publications found

Genes affected

ENSG00000285837 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378327	XR_946002.3	n.161-13583G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285837	ENST00000647733.1	c.1129+15456C>T		intron_variant	Intron 5 of 7			ENSP00000502188.1
LINC02929	ENST00000395251.5	n.151-5036C>T		intron_variant	Intron 1 of 6	1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45171 AN: 151978 Hom.: 7976 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.297 AC: 45157 AN: 152096 Hom.: 7974 Cov.: 31 AF XY: 0.298 AC XY: 22170 AN XY: 74352

African (AFR) AF: 0.123 AC: 5100 AN: 41494

American (AMR) AF: 0.220 AC: 3370 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1376 AN: 3472

East Asian (EAS) AF: 0.587 AC: 3037 AN: 5176

South Asian (SAS) AF: 0.380 AC: 1833 AN: 4818

European-Finnish (FIN) AF: 0.367 AC: 3876 AN: 10558

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.374 AC: 25444 AN: 67974

Other (OTH) AF: 0.294 AC: 622 AN: 2114

Alfa AF: 0.342 Hom.: 37631

Bravo AF: 0.277

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.32
DANN	Benign	0.47
PhyloP100		-1.6
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: rs10995251; hg19: chr10-64398466;