chr10-62666296-G-T

Position:

• chr10-62666296-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The XM_047426120.1(LOC124902436):​c.406+94G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 786,182 control chromosomes in the GnomAD database, including 43,641 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.37 (11304 hom., cov: 31)
  • Exomes 𝑓: 0.31 (32337 hom.)
• Consequence: LOC124902436 XM_047426120.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.121

Genes affected

LOC124902436 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 10-62666296-G-T is Benign according to our data. Variant chr10-62666296-G-T is described in ClinVar as [Benign]. Clinvar id is 1258627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902436	XM_047426120.1	c.406+94G>T		intron_variant			XP_047282076.1
LOC124902436	XM_047426118.1	c.562+94G>T		intron_variant			XP_047282074.1
LOC124902436	XM_047426121.1	c.712+94G>T		intron_variant			XP_047282077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000344640.7	n.371-3911G>T		intron_variant, non_coding_transcript_variant		1
LINC02929	ENST00000373784.6	n.444+94G>T		intron_variant, non_coding_transcript_variant		1
LINC02929	ENST00000395249.5	n.265+94G>T		intron_variant, non_coding_transcript_variant		1
LINC02929	ENST00000395251.5	n.890+94G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55628 AN: 151640 Hom.: 11281 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.361

GnomAD4 exome AF: 0.307 AC: 194942 AN: 634424 Hom.: 32337 AF XY: 0.312 AC XY: 104309 AN XY: 334738

Gnomad4 AFR exome AF: 0.527

Gnomad4 AMR exome AF: 0.475

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.275

Gnomad4 SAS exome AF: 0.424

Gnomad4 FIN exome AF: 0.307

Gnomad4 NFE exome AF: 0.276

Gnomad4 OTH exome AF: 0.322

GnomAD4 genome AF: 0.367 AC: 55703 AN: 151758 Hom.: 11304 Cov.: 31 AF XY: 0.371 AC XY: 27544 AN XY: 74180

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.360

Alfa AF: 0.321 Hom.: 3527

Bravo AF: 0.383

Asia WGS AF: 0.353 AC: 1228 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	clinical testing	GeneDx	May 16, 2021	- -
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	-0.86
CADD	Benign	1.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4746516; hg19: chr10-64426056; COSMIC: COSV60823844;