rs10995251

chr10-62638706-C-T

Variant summary

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

The ENST00000395251.5(LINC02929):n.151-5036C>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 0.297 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: LINC02929 ENST00000395251.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

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

LOC105378327 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105378327	XR_946002.3	n.161-13583G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02929	ENST00000395251.5	n.151-5036C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.294

Alfa AF: 0.353 Hom.: 16374

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10995251; hg19: chr10-64398466;