rs2837237

chr21-39825930-T-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 0.12 in 152,158 control chromosomes in the GnomAD database, including 1,074 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 0.12 (1074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

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 (AFR) allele frequency at 95% confidence interval = 0.139 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: 0.120 AC: 18280 AN: 152040 Hom.: 1072 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.0768

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.120 AC: 18301 AN: 152158 Hom.: 1074 Cov.: 32 AF XY: 0.119 AC XY: 8844 AN XY: 74398

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0994

Gnomad4 ASJ AF: 0.0768

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.128

Alfa AF: 0.116 Hom.: 1321

Bravo AF: 0.122

Asia WGS AF: 0.130 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2837237; hg19: chr21-41197857;