rs9981660

Variant names:

• chr21-42317828-G-A
• rs9981660

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 0.111 in 152,220 control chromosomes in the GnomAD database, including 1,755 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 0.11 (1755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.111 AC: 16926 AN: 152102 Hom.: 1746 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0451

Gnomad FIN AF: 0.0198

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0446

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.111 AC: 16965 AN: 152220 Hom.: 1755 Cov.: 32 AF XY: 0.109 AC XY: 8080 AN XY: 74422

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.0804

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.0443

Gnomad4 FIN AF: 0.0198

Gnomad4 NFE AF: 0.0446

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.0541 Hom.: 476

Bravo AF: 0.124

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9981660; hg19: chr21-43737938;