21-44985540-C-T

Variant names:

• chr21-44985540-C-T
• rs11702235

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 0.146 in 152,218 control chromosomes in the GnomAD database, including 1,745 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 0.15 (1745 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 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: 0.146 AC: 22269 AN: 152100 Hom.: 1748 Cov.: 34

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.146 AC: 22270 AN: 152218 Hom.: 1745 Cov.: 34 AF XY: 0.147 AC XY: 10946 AN XY: 74408

African (AFR) AF: 0.122 AC: 5076 AN: 41530

American (AMR) AF: 0.209 AC: 3204 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3472

East Asian (EAS) AF: 0.110 AC: 568 AN: 5184

South Asian (SAS) AF: 0.0566 AC: 273 AN: 4826

European-Finnish (FIN) AF: 0.153 AC: 1629 AN: 10614

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10379 AN: 67974

Other (OTH) AF: 0.129 AC: 273 AN: 2116

Alfa AF: 0.155 Hom.: 238

Bravo AF: 0.152

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.84
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs11702235; hg19: chr21-46405455;