rs9980664

Variant names:

• chr21-33362204-C-A
• rs9980664

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 0.193 in 152,030 control chromosomes in the GnomAD database, including 3,084 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 0.19 (3084 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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: 0.192 AC: 29238 AN: 151912 Hom.: 3074 Cov.: 31

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0925

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.193 AC: 29269 AN: 152030 Hom.: 3084 Cov.: 31 AF XY: 0.194 AC XY: 14412 AN XY: 74294

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.209

Alfa AF: 0.179 Hom.: 1381

Bravo AF: 0.204

Asia WGS AF: 0.327 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9980664; hg19: chr21-34734510;