rs10984103

Variant names:

• chr9-97876993-A-C
• rs10984103

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 0.682 in 151,974 control chromosomes in the GnomAD database, including 35,757 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 0.68 (35757 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.682 AC: 103590 AN: 151856 Hom.: 35721 Cov.: 31

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.682 AC: 103670 AN: 151974 Hom.: 35757 Cov.: 31 AF XY: 0.686 AC XY: 50926 AN XY: 74290

African (AFR) AF: 0.761 AC: 31531 AN: 41426

American (AMR) AF: 0.681 AC: 10401 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2196 AN: 3468

East Asian (EAS) AF: 0.922 AC: 4751 AN: 5154

South Asian (SAS) AF: 0.674 AC: 3245 AN: 4818

European-Finnish (FIN) AF: 0.647 AC: 6831 AN: 10558

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42677 AN: 67960

Other (OTH) AF: 0.684 AC: 1447 AN: 2114

Alfa AF: 0.669 Hom.: 29808

Bravo AF: 0.691

Asia WGS AF: 0.779 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	15
DANN	Benign	0.70
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10984103; hg19: chr9-100639275;