chr21-39849374-G-A

Variant names:

• chr21-39849374-G-A
• rs2837254

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 0.172 in 152,026 control chromosomes in the GnomAD database, including 3,048 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 0.17 (3048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 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: 0.171 AC: 26038 AN: 151908 Hom.: 3041 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0737

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.172 AC: 26078 AN: 152026 Hom.: 3048 Cov.: 32 AF XY: 0.168 AC XY: 12507 AN XY: 74314

African (AFR) AF: 0.340 AC: 14065 AN: 41416

American (AMR) AF: 0.119 AC: 1816 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0737 AC: 256 AN: 3472

East Asian (EAS) AF: 0.108 AC: 558 AN: 5172

South Asian (SAS) AF: 0.101 AC: 484 AN: 4804

European-Finnish (FIN) AF: 0.101 AC: 1068 AN: 10582

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7323 AN: 67986

Other (OTH) AF: 0.167 AC: 352 AN: 2114

Alfa AF: 0.121 Hom.: 1414

Bravo AF: 0.181

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.11
DANN	Benign	0.83
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2837254; hg19: chr21-41221301;