chr10-62666038-C-T

Position:

• chr10-62666038-C-T

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4 BP6_Very_Strong BA1

The XM_047426120.1(LOC124902436):​c.333-91C>T variant causes a intron change. The variant allele was found at a frequency of 0.00495 in 862,834 control chromosomes in the GnomAD database, including 145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.019 (108 hom., cov: 32)
  • Exomes 𝑓: 0.0020 (37 hom.)
• Consequence: LOC124902436 XM_047426120.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 3.90

Genes affected

LOC124902436 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BP6: Variant 10-62666038-C-T is Benign according to our data. Variant chr10-62666038-C-T is described in ClinVar as [Benign]. Clinvar id is 1234400.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902436	XM_047426120.1	c.333-91C>T		intron_variant			XP_047282076.1
LOC124902436	XM_047426118.1	c.489-91C>T		intron_variant			XP_047282074.1
LOC124902436	XM_047426121.1	c.639-91C>T		intron_variant			XP_047282077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000344640.7	n.371-4169C>T		intron_variant, non_coding_transcript_variant		1
LINC02929	ENST00000373784.6	n.371-91C>T		intron_variant, non_coding_transcript_variant		1
LINC02929	ENST00000395249.5	n.192-91C>T		intron_variant, non_coding_transcript_variant		1
LINC02929	ENST00000395251.5	n.817-91C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0188 AC: 2852 AN: 151690 Hom.: 106 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00932

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000416

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.000294

Gnomad OTH AF: 0.0153

GnomAD4 exome AF: 0.00197 AC: 1403 AN: 711026 Hom.: 37 AF XY: 0.00174 AC XY: 649 AN XY: 373280

Gnomad4 AFR exome AF: 0.0642

Gnomad4 AMR exome AF: 0.00470

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000245

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000165

Gnomad4 OTH exome AF: 0.00513

GnomAD4 genome AF: 0.0189 AC: 2868 AN: 151808 Hom.: 108 Cov.: 32 AF XY: 0.0182 AC XY: 1353 AN XY: 74202

Gnomad4 AFR AF: 0.0644

Gnomad4 AMR AF: 0.00930

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000416

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000294

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.0139 Hom.: 6

Bravo AF: 0.0214

Asia WGS AF: 0.00606 AC: 22 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 26, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	18
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs111695652; hg19: chr10-64425798;