21-41139991-T-G

Variant names:

• chr21-41139991-T-G
• rs2837960

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 0.214 in 152,214 control chromosomes in the GnomAD database, including 3,729 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 0.21 (3729 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32535 AN: 152096 Hom.: 3729 Cov.: 33

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.214 AC: 32550 AN: 152214 Hom.: 3729 Cov.: 33 AF XY: 0.213 AC XY: 15851 AN XY: 74416

African (AFR) AF: 0.306 AC: 12687 AN: 41504

American (AMR) AF: 0.155 AC: 2369 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3470

East Asian (EAS) AF: 0.192 AC: 991 AN: 5168

South Asian (SAS) AF: 0.175 AC: 843 AN: 4826

European-Finnish (FIN) AF: 0.189 AC: 2002 AN: 10616

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12079 AN: 68012

Other (OTH) AF: 0.208 AC: 440 AN: 2112

Alfa AF: 0.187 Hom.: 11817

Bravo AF: 0.215

Asia WGS AF: 0.173 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.19
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2837960; hg19: chr21-42511918;