10-62670472-C-A

Position:

• chr10-62670472-C-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.*171C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00745 in 571,208 control chromosomes in the GnomAD database, including 160 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.021 (134 hom., cov: 32)
  • Exomes 𝑓: 0.0026 (26 hom.)
• Consequence: LOC124902436 XM_047426120.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.305

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=-0.89).
• BP6: Variant 10-62670472-C-A is Benign according to our data. Variant chr10-62670472-C-A is described in ClinVar as [Benign]. Clinvar id is 1225274.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902436	XM_047426120.1	c.*171C>A		3_prime_UTR_variant	6/6		XP_047282076.1
LOC124902436	XM_047426118.1	c.*171C>A		3_prime_UTR_variant	6/6		XP_047282074.1
LOC124902436	XM_047426121.1	c.*171C>A		3_prime_UTR_variant	6/6		XP_047282077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02929	ENST00000395251.5	n.1156C>A		non_coding_transcript_exon_variant	7/7	1

Frequencies

GnomAD3 genomes AF: 0.0207 AC: 3155 AN: 152068 Hom.: 133 Cov.: 32

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.0191

GnomAD4 exome AF: 0.00259 AC: 1086 AN: 419022 Hom.: 26 Cov.: 4 AF XY: 0.00209 AC XY: 465 AN XY: 222634

Gnomad4 AFR exome AF: 0.0685

Gnomad4 AMR exome AF: 0.00490

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000233

Gnomad4 FIN exome AF: 0.0000732

Gnomad4 NFE exome AF: 0.000219

Gnomad4 OTH exome AF: 0.00514

GnomAD4 genome AF: 0.0208 AC: 3168 AN: 152186 Hom.: 134 Cov.: 32 AF XY: 0.0197 AC XY: 1467 AN XY: 74406

Gnomad4 AFR AF: 0.0711

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.000309

Gnomad4 OTH AF: 0.0189

Alfa AF: 0.00341 Hom.: 3

Bravo AF: 0.0238

Asia WGS AF: 0.00520 AC: 18 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 22, 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	-0.89
CADD	Benign	1.9
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: rs114275831; hg19: chr10-64430232;