21-20971699-T-C

Variant names:

• chr21-20971699-T-C
• rs2826629

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 0.346 in 151,946 control chromosomes in the GnomAD database, including 9,329 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 0.35 (9329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52479 AN: 151828 Hom.: 9324 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.346 AC: 52518 AN: 151946 Hom.: 9329 Cov.: 32 AF XY: 0.345 AC XY: 25617 AN XY: 74266

African (AFR) AF: 0.336 AC: 13914 AN: 41452

American (AMR) AF: 0.321 AC: 4897 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3464

East Asian (EAS) AF: 0.145 AC: 747 AN: 5166

South Asian (SAS) AF: 0.376 AC: 1811 AN: 4818

European-Finnish (FIN) AF: 0.357 AC: 3753 AN: 10526

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 25008 AN: 67958

Other (OTH) AF: 0.354 AC: 748 AN: 2112

Alfa AF: 0.361 Hom.: 5004

Bravo AF: 0.340

Asia WGS AF: 0.285 AC: 989 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2826629; hg19: chr21-22344016;