chr10-62656530-A-G

Position:

• chr10-62656530-A-G

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.332+44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 767,418 control chromosomes in the GnomAD database, including 6,292 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.095 (1017 hom., cov: 32)
  • Exomes 𝑓: 0.12 (5275 hom.)
• Consequence: LOC124902436 XM_047426120.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.170

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=-0.85).
• BP6: Variant 10-62656530-A-G is Benign according to our data. Variant chr10-62656530-A-G is described in ClinVar as [Benign]. Clinvar id is 1283038.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902436	XM_047426120.1	c.332+44A>G		intron_variant			XP_047282076.1
LOC124902436	XM_047426118.1	c.488+44A>G		intron_variant			XP_047282074.1
LOC124902436	XM_047426119.1	c.488+44A>G		intron_variant			XP_047282075.1
LOC124902436	XM_047426121.1	c.638+44A>G		intron_variant			XP_047282077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5	n.816+44A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0954 AC: 14497 AN: 151998 Hom.: 1017 Cov.: 32

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0805

GnomAD3 exomes AF: 0.103 AC: 25274 AN: 245924 Hom.: 1752 AF XY: 0.104 AC XY: 13874 AN XY: 133064

Gnomad AFR exome AF: 0.0195

Gnomad AMR exome AF: 0.0426

Gnomad ASJ exome AF: 0.140

Gnomad EAS exome AF: 0.000331

Gnomad SAS exome AF: 0.0501

Gnomad FIN exome AF: 0.185

Gnomad NFE exome AF: 0.145

Gnomad OTH exome AF: 0.113

GnomAD4 exome AF: 0.116 AC: 71573 AN: 615302 Hom.: 5275 Cov.: 0 AF XY: 0.114 AC XY: 38267 AN XY: 334914

Gnomad4 AFR exome AF: 0.0216

Gnomad4 AMR exome AF: 0.0449

Gnomad4 ASJ exome AF: 0.142

Gnomad4 EAS exome AF: 0.000224

Gnomad4 SAS exome AF: 0.0502

Gnomad4 FIN exome AF: 0.182

Gnomad4 NFE exome AF: 0.145

Gnomad4 OTH exome AF: 0.110

GnomAD4 genome AF: 0.0953 AC: 14494 AN: 152116 Hom.: 1017 Cov.: 32 AF XY: 0.0953 AC XY: 7085 AN XY: 74360

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.0553

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.000968

Gnomad4 SAS AF: 0.0448

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.118 Hom.: 497

Bravo AF: 0.0823

Asia WGS AF: 0.0310 AC: 108 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 16, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12776269; hg19: chr10-64416290; COSMIC: COSV60823955;