9-100726346-G-A

Variant names:

• chr9-100726346-G-A
• rs10521051

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 0.0528 in 152,194 control chromosomes in the GnomAD database, including 580 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 0.053 (580 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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: 0.0527 AC: 8020 AN: 152076 Hom.: 581 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0200

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0528 AC: 8036 AN: 152194 Hom.: 580 Cov.: 32 AF XY: 0.0605 AC XY: 4504 AN XY: 74420

African (AFR) AF: 0.0414 AC: 1719 AN: 41518

American (AMR) AF: 0.0695 AC: 1063 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1967 AN: 5176

South Asian (SAS) AF: 0.150 AC: 724 AN: 4828

European-Finnish (FIN) AF: 0.0879 AC: 931 AN: 10588

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0200 AC: 1358 AN: 67996

Other (OTH) AF: 0.0578 AC: 122 AN: 2110

Alfa AF: 0.0155 Hom.: 8

Bravo AF: 0.0533

Asia WGS AF: 0.271 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10521051; hg19: chr9-103488628;