chr21-30101474-C-T

Variant names:

• chr21-30101474-C-T
• rs2832616

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 0.203 in 151,902 control chromosomes in the GnomAD database, including 4,097 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 0.20 (4097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 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: 0.203 AC: 30786 AN: 151784 Hom.: 4092 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.0647

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.203 AC: 30812 AN: 151902 Hom.: 4097 Cov.: 32 AF XY: 0.199 AC XY: 14804 AN XY: 74234

African (AFR) AF: 0.374 AC: 15495 AN: 41412

American (AMR) AF: 0.129 AC: 1967 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3464

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5154

South Asian (SAS) AF: 0.273 AC: 1310 AN: 4802

European-Finnish (FIN) AF: 0.0647 AC: 684 AN: 10580

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9260 AN: 67932

Other (OTH) AF: 0.191 AC: 402 AN: 2106

Alfa AF: 0.159 Hom.: 1373

Bravo AF: 0.212

Asia WGS AF: 0.254 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
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: rs2832616; hg19: chr21-31473792;