10-62277122-G-C

Position:

• chr10-62277122-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.3 in 151,700 control chromosomes in the GnomAD database, including 7,840 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7840 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.62277122G>C		intergenic_region
LINC02621	NR_186389.1	n.86-12399G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45393 AN: 151584 Hom.: 7819 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0981

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.269

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.300 AC: 45476 AN: 151700 Hom.: 7840 Cov.: 31 AF XY: 0.297 AC XY: 22015 AN XY: 74170

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.0983

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.272

Alfa AF: 0.145 Hom.: 249

Bravo AF: 0.304

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6479800; hg19: chr10-64036881;