chr21-39931256-G-A

Variant names:

• chr21-39931256-G-A
• rs2837297

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 0.18 in 152,050 control chromosomes in the GnomAD database, including 2,472 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 0.18 (2472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 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: 0.180 AC: 27390 AN: 151932 Hom.: 2475 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.180 AC: 27408 AN: 152050 Hom.: 2472 Cov.: 32 AF XY: 0.178 AC XY: 13269 AN XY: 74338

African (AFR) AF: 0.198 AC: 8189 AN: 41442

American (AMR) AF: 0.197 AC: 3001 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1037 AN: 5156

South Asian (SAS) AF: 0.134 AC: 645 AN: 4812

European-Finnish (FIN) AF: 0.130 AC: 1377 AN: 10600

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11871 AN: 67988

Other (OTH) AF: 0.188 AC: 397 AN: 2108

Alfa AF: 0.178 Hom.: 2256

Bravo AF: 0.189

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.64
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2837297; hg19: chr21-41303181;