rs10985375

Variant names:

• chr9-121787363-C-A
• rs10985375

Your query was ambiguous. Multiple possible variants found:

• chr9-121787363-C-A
• chr9-121787363-C-G
• chr9-121787363-C-T

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 0.14 in 151,974 control chromosomes in the GnomAD database, including 1,640 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 0.14 (1640 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 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: 0.140 AC: 21302 AN: 151856 Hom.: 1644 Cov.: 29

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.140 AC: 21299 AN: 151974 Hom.: 1640 Cov.: 29 AF XY: 0.140 AC XY: 10421 AN XY: 74270

African (AFR) AF: 0.0902 AC: 3740 AN: 41462

American (AMR) AF: 0.153 AC: 2344 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1096 AN: 5144

South Asian (SAS) AF: 0.151 AC: 726 AN: 4804

European-Finnish (FIN) AF: 0.159 AC: 1675 AN: 10558

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10588 AN: 67952

Other (OTH) AF: 0.156 AC: 329 AN: 2106

Alfa AF: 0.123 Hom.: 493

Bravo AF: 0.140

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.077
DANN	Benign	0.79
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs10985375; hg19: chr9-124549642;