rs2187102

chr21-36992685-G-Achr21-36992685-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 0.256 in 152,080 control chromosomes in the GnomAD database, including 5,164 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 0.26 (5164 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38979 AN: 151962 Hom.: 5155 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.256 AC: 39002 AN: 152080 Hom.: 5164 Cov.: 33 AF XY: 0.256 AC XY: 19004 AN XY: 74360

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.246

Alfa AF: 0.270 Hom.: 3308

Bravo AF: 0.246

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	5.3
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2187102; hg19: chr21-38364985;