10-62636035-T-C

Position:

• chr10-62636035-T-C

Variant summary

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

The ENST00000395251.5(LINC02929):​n.151-7707T>C 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 0.847 in 152,254 control chromosomes in the GnomAD database, including 55,063 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 0.85 (55063 hom., cov: 33)
• Consequence: LINC02929 ENST00000395251.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378327	XR_946002.3	n.161-10912A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5	n.151-7707T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128811 AN: 152136 Hom.: 55000 Cov.: 33

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.847 AC: 128933 AN: 152254 Hom.: 55063 Cov.: 33 AF XY: 0.849 AC XY: 63187 AN XY: 74444

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.819

Alfa AF: 0.799 Hom.: 29707

Bravo AF: 0.854

Asia WGS AF: 0.876 AC: 3047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
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: rs10740085; hg19: chr10-64395795;