9-103874752-C-T

Variant names:

• chr9-103874752-C-T
• rs10820559

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 0.595 in 151,532 control chromosomes in the GnomAD database, including 27,393 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 0.60 (27393 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 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: 0.595 AC: 90153 AN: 151414 Hom.: 27397 Cov.: 29

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.595 AC: 90170 AN: 151532 Hom.: 27393 Cov.: 29 AF XY: 0.599 AC XY: 44293 AN XY: 73994

African (AFR) AF: 0.492 AC: 20262 AN: 41218

American (AMR) AF: 0.520 AC: 7918 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2199 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2586 AN: 5138

South Asian (SAS) AF: 0.640 AC: 3052 AN: 4772

European-Finnish (FIN) AF: 0.730 AC: 7681 AN: 10524

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.656 AC: 44530 AN: 67896

Other (OTH) AF: 0.582 AC: 1222 AN: 2098

Alfa AF: 0.631 Hom.: 129861

Bravo AF: 0.571

Asia WGS AF: 0.563 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10820559; hg19: chr9-106637033;