rs10228566

Positions:

• chr7-113097501-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.177 in 152,042 control chromosomes in the GnomAD database, including 2,578 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 0.18 (2578 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26848 AN: 151924 Hom.: 2570 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0835

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.177 AC: 26875 AN: 152042 Hom.: 2578 Cov.: 32 AF XY: 0.176 AC XY: 13105 AN XY: 74326

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0833

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.165

Alfa AF: 0.171 Hom.: 763

Bravo AF: 0.172

Asia WGS AF: 0.183 AC: 640 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	0.055
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10228566; hg19: chr7-112737556;