rs10223625

Variant names:

• chr6-66417061-A-G
• rs10223625

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 0.119 in 151,686 control chromosomes in the GnomAD database, including 1,203 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 0.12 (1203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 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: 0.119 AC: 18067 AN: 151568 Hom.: 1203 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0111

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.119 AC: 18080 AN: 151686 Hom.: 1203 Cov.: 32 AF XY: 0.118 AC XY: 8779 AN XY: 74128

African (AFR) AF: 0.153 AC: 6360 AN: 41444

American (AMR) AF: 0.0639 AC: 971 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3458

East Asian (EAS) AF: 0.0111 AC: 57 AN: 5122

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1550 AN: 10580

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8205 AN: 67752

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.125 Hom.: 165

Bravo AF: 0.115

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.45
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs10223625; hg19: chr6-67126954;