chr10-62655271-G-A

Position:

• chr10-62655271-G-A

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.127-96G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,479,830 control chromosomes in the GnomAD database, including 24,088 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.21 (3785 hom., cov: 32)
  • Exomes 𝑓: 0.16 (20303 hom.)
• Consequence: LOC124902436 XM_047426120.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0230

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=-0.82).
• BP6: Variant 10-62655271-G-A is Benign according to our data. Variant chr10-62655271-G-A is described in ClinVar as [Benign]. Clinvar id is 1257178.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902436	XM_047426120.1	c.127-96G>A		intron_variant			XP_047282076.1
LOC105378327	XR_946002.3	n.160+155C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5	n.461-96G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31780 AN: 151942 Hom.: 3773 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.196

GnomAD4 exome AF: 0.164 AC: 218067 AN: 1327770 Hom.: 20303 AF XY: 0.165 AC XY: 108329 AN XY: 656790

Gnomad4 AFR exome AF: 0.294

Gnomad4 AMR exome AF: 0.383

Gnomad4 ASJ exome AF: 0.156

Gnomad4 EAS exome AF: 0.272

Gnomad4 SAS exome AF: 0.229

Gnomad4 FIN exome AF: 0.158

Gnomad4 NFE exome AF: 0.145

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.209 AC: 31827 AN: 152060 Hom.: 3785 Cov.: 32 AF XY: 0.212 AC XY: 15767 AN XY: 74334

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.196

Alfa AF: 0.176 Hom.: 639

Bravo AF: 0.226

Asia WGS AF: 0.247 AC: 857 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	-0.82
CADD	Benign	0.81
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10822043; hg19: chr10-64415031; COSMIC: COSV60823842;