21-27100170-A-G

Variant names:

• chr21-27100170-A-G
• rs10482982

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 0.0571 in 152,334 control chromosomes in the GnomAD database, including 322 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 0.057 (322 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 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: 0.0571 AC: 8691 AN: 152216 Hom.: 320 Cov.: 33

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.0498

Gnomad EAS AF: 0.00288

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0571 AC: 8698 AN: 152334 Hom.: 322 Cov.: 33 AF XY: 0.0569 AC XY: 4241 AN XY: 74500

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0498

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0603

Gnomad4 NFE AF: 0.0816

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0733 Hom.: 571

Bravo AF: 0.0514

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10482982; hg19: chr21-28472489;