rs10223593

Variant names:

• chr6-66416455-A-G
• rs10223593

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 151,794 control chromosomes in the GnomAD database, including 1,205 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 (1205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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: 18088 AN: 151678 Hom.: 1205 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.0420

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: 18100 AN: 151794 Hom.: 1205 Cov.: 32 AF XY: 0.119 AC XY: 8793 AN XY: 74200

African (AFR) AF: 0.154 AC: 6373 AN: 41470

American (AMR) AF: 0.0638 AC: 970 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 389 AN: 3456

East Asian (EAS) AF: 0.0111 AC: 57 AN: 5148

South Asian (SAS) AF: 0.0425 AC: 205 AN: 4826

European-Finnish (FIN) AF: 0.147 AC: 1561 AN: 10594

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

European-Non Finnish (NFE) AF: 0.121 AC: 8204 AN: 67776

Other (OTH) AF: 0.108 AC: 228 AN: 2116

Alfa AF: 0.125 Hom.: 165

Bravo AF: 0.115

Asia WGS AF: 0.0420 AC: 145 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.95
DANN	Benign	0.39
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs10223593; hg19: chr6-67126348;