rs10223721

Variant names:

• chr6-66416563-G-A
• rs10223721

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 0.12 in 151,600 control chromosomes in the GnomAD database, including 1,222 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 (1222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• 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: 0.120 AC: 18124 AN: 151482 Hom.: 1222 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0109

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.149

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: 0.120 AC: 18137 AN: 151600 Hom.: 1222 Cov.: 32 AF XY: 0.119 AC XY: 8811 AN XY: 74112

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0639

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0109

Gnomad4 SAS AF: 0.0427

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.108

Alfa AF: 0.118 Hom.: 191

Bravo AF: 0.115

Asia WGS AF: 0.0410 AC: 144 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10223721; hg19: chr6-67126456;