rs10228566

Variant names:

• chr7-113097501-G-A
• rs10228566

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 0.177 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.208 AC: 8637 AN: 41474

American (AMR) AF: 0.104 AC: 1583 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3472

East Asian (EAS) AF: 0.0833 AC: 430 AN: 5164

South Asian (SAS) AF: 0.322 AC: 1556 AN: 4826

European-Finnish (FIN) AF: 0.129 AC: 1368 AN: 10580

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12191 AN: 67952

Other (OTH) AF: 0.165 AC: 347 AN: 2106

Alfa AF: 0.173 Hom.: 968

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10228566; hg19: chr7-112737556;