10-62655641-G-C

Position:

• chr10-62655641-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Moderate BP6_Very_Strong BS2

The XM_047426120.1(LOC124902436):​c.241+160G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00361 in 1,613,524 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0026 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0037 (15 hom.)
• Consequence: LOC124902436 XM_047426120.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 2.97

Genes affected

LOC124902436 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BP6: Variant 10-62655641-G-C is Benign according to our data. Variant chr10-62655641-G-C is described in ClinVar as [Benign]. Clinvar id is 782150.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAdExome4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902436	XM_047426120.1	c.241+160G>C		intron_variant			XP_047282076.1
LOC124902436	XM_047426118.1	c.397+160G>C		intron_variant			XP_047282074.1
LOC124902436	XM_047426119.1	c.397+160G>C		intron_variant			XP_047282075.1
LOC124902436	XM_047426121.1	c.547+10G>C		intron_variant			XP_047282077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5	n.725+10G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.00257 AC: 391 AN: 152098 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000845

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.00321

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00375

Gnomad OTH AF: 0.00239

GnomAD3 exomes AF: 0.00255 AC: 636 AN: 249850 Hom.: 1 AF XY: 0.00249 AC XY: 337 AN XY: 135098

Gnomad AFR exome AF: 0.000620

Gnomad AMR exome AF: 0.00263

Gnomad ASJ exome AF: 0.00240

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00121

Gnomad FIN exome AF: 0.000371

Gnomad NFE exome AF: 0.00399

Gnomad OTH exome AF: 0.00262

GnomAD4 exome AF: 0.00372 AC: 5430 AN: 1461308 Hom.: 15 Cov.: 44 AF XY: 0.00360 AC XY: 2617 AN XY: 726868

Gnomad4 AFR exome AF: 0.000628

Gnomad4 AMR exome AF: 0.00273

Gnomad4 ASJ exome AF: 0.00234

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00124

Gnomad4 FIN exome AF: 0.000431

Gnomad4 NFE exome AF: 0.00439

Gnomad4 OTH exome AF: 0.00346

GnomAD4 genome AF: 0.00257 AC: 391 AN: 152216 Hom.: 1 Cov.: 32 AF XY: 0.00227 AC XY: 169 AN XY: 74416

Gnomad4 AFR AF: 0.000843

Gnomad4 AMR AF: 0.00321

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00125

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.00375

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.000972 Hom.: 0

Bravo AF: 0.00281

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 11, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	19
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs146014775; hg19: chr10-64415401;