rs2823097

Positions:

• chr21-15150823-G-C
• chr21-15150823-G-T

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 0.502 in 152,142 control chromosomes in the GnomAD database, including 22,608 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 0.50 (22608 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.15150823G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76277 AN: 152024 Hom.: 22520 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.502 AC: 76441 AN: 152142 Hom.: 22608 Cov.: 32 AF XY: 0.505 AC XY: 37588 AN XY: 74370

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.482

Alfa AF: 0.241 Hom.: 523

Bravo AF: 0.526

Asia WGS AF: 0.556 AC: 1934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	10
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823097; hg19: chr21-16523144;