rs2853215

Variant names:

• chr20-3685608-G-A
• rs2853215

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.232 in 152,132 control chromosomes in the GnomAD database, including 4,471 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 0.23 (4471 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35292 AN: 152014 Hom.: 4461 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.232 AC: 35316 AN: 152132 Hom.: 4471 Cov.: 32 AF XY: 0.231 AC XY: 17194 AN XY: 74382

African (AFR) AF: 0.121 AC: 5024 AN: 41536

American (AMR) AF: 0.270 AC: 4126 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1209 AN: 5162

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4818

European-Finnish (FIN) AF: 0.251 AC: 2656 AN: 10584

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19100 AN: 67968

Other (OTH) AF: 0.237 AC: 500 AN: 2110

Alfa AF: 0.257 Hom.: 11502

Bravo AF: 0.227

Asia WGS AF: 0.311 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.4
DANN	Benign	0.82
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs2853215; hg19: chr20-3666255;