rs9978224

Variant names:

• chr21-39937898-G-A
• rs9978224

Your query was ambiguous. Multiple possible variants found:

• chr21-39937898-G-A
• chr21-39937898-G-C

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 0.324 in 152,024 control chromosomes in the GnomAD database, including 8,468 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 0.32 (8468 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 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: 0.324 AC: 49267 AN: 151904 Hom.: 8452 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.324 AC: 49326 AN: 152024 Hom.: 8468 Cov.: 32 AF XY: 0.325 AC XY: 24131 AN XY: 74294

African (AFR) AF: 0.444 AC: 18420 AN: 41440

American (AMR) AF: 0.305 AC: 4669 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1985 AN: 5144

South Asian (SAS) AF: 0.253 AC: 1221 AN: 4818

European-Finnish (FIN) AF: 0.292 AC: 3084 AN: 10560

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18139 AN: 67974

Other (OTH) AF: 0.302 AC: 639 AN: 2114

Alfa AF: 0.279 Hom.: 13414

Bravo AF: 0.334

Asia WGS AF: 0.330 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs9978224; hg19: chr21-41309823;