chr21-44985540-C-T

Variant names:

• chr21-44985540-C-T
• rs11702235

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 0.146 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.146 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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0566

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.129

Alfa AF: 0.156 Hom.: 228

Bravo AF: 0.152

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11702235; hg19: chr21-46405455;