rs9978374

Positions:

• chr21-14447400-C-T
• chrNW_003315967.2-35845-T-C

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 0.566 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.14447400C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.572

Alfa AF: 0.580 Hom.: 18912

Bravo AF: 0.557

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9978374; hg19: chr21-15819721;