rs9978374

Variant names:

• chr21-14447400-C-T
• rs9978374

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 0.566 in 151,996 control chromosomes in the GnomAD database, including 24,500 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 0.57 (24500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86026 AN: 151878 Hom.: 24487 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.566 AC: 86071 AN: 151996 Hom.: 24500 Cov.: 32 AF XY: 0.566 AC XY: 42057 AN XY: 74266

African (AFR) AF: 0.551 AC: 22867 AN: 41468

American (AMR) AF: 0.491 AC: 7487 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2312 AN: 3462

East Asian (EAS) AF: 0.583 AC: 3008 AN: 5158

South Asian (SAS) AF: 0.584 AC: 2811 AN: 4814

European-Finnish (FIN) AF: 0.593 AC: 6260 AN: 10562

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.581 AC: 39505 AN: 67970

Other (OTH) AF: 0.572 AC: 1205 AN: 2108

Alfa AF: 0.575 Hom.: 30162

Bravo AF: 0.557

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.059
DANN	Benign	0.73
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9978374; hg19: chr21-15819721;