rs10511467

Variant names:

• chr9-7373051-G-A
• rs10511467

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 0.13 in 152,148 control chromosomes in the GnomAD database, including 1,616 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 0.13 (1616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.165 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: 0.131 AC: 19840 AN: 152030 Hom.: 1615 Cov.: 32

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0956

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.130 AC: 19835 AN: 152148 Hom.: 1616 Cov.: 32 AF XY: 0.134 AC XY: 9960 AN XY: 74390

African (AFR) AF: 0.0364 AC: 1513 AN: 41514

American (AMR) AF: 0.171 AC: 2611 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 563 AN: 3464

East Asian (EAS) AF: 0.0949 AC: 491 AN: 5176

South Asian (SAS) AF: 0.170 AC: 821 AN: 4816

European-Finnish (FIN) AF: 0.191 AC: 2024 AN: 10576

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11242 AN: 67998

Other (OTH) AF: 0.127 AC: 269 AN: 2114

Alfa AF: 0.157 Hom.: 1143

Bravo AF: 0.125

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs10511467; hg19: chr9-7373051;