rs10499728

Variant names:

• chr7-54062906-G-A
• rs10499728

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 0.188 in 151,886 control chromosomes in the GnomAD database, including 3,110 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 0.19 (3110 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.234 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: 0.188 AC: 28481 AN: 151766 Hom.: 3106 Cov.: 33

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0590

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.188 AC: 28507 AN: 151886 Hom.: 3110 Cov.: 33 AF XY: 0.192 AC XY: 14281 AN XY: 74210

African (AFR) AF: 0.0971 AC: 4027 AN: 41452

American (AMR) AF: 0.179 AC: 2734 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3466

East Asian (EAS) AF: 0.0592 AC: 306 AN: 5172

South Asian (SAS) AF: 0.212 AC: 1016 AN: 4802

European-Finnish (FIN) AF: 0.302 AC: 3171 AN: 10502

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16075 AN: 67944

Other (OTH) AF: 0.159 AC: 335 AN: 2112

Alfa AF: 0.202 Hom.: 552

Bravo AF: 0.173

Asia WGS AF: 0.130 AC: 449 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	10
DANN	Benign	0.46
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10499728; hg19: chr7-54130599;