rs12206223

Variant names:

• chr6-102521031-T-C
• rs12206223

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 0.0452 in 151,774 control chromosomes in the GnomAD database, including 196 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 0.045 (196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0645 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: 0.0453 AC: 6867 AN: 151656 Hom.: 196 Cov.: 32

Gnomad AFR AF: 0.0121

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0826

Gnomad EAS AF: 0.00369

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.0638

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

GnomAD4 genome AF: 0.0452 AC: 6863 AN: 151774 Hom.: 196 Cov.: 32 AF XY: 0.0441 AC XY: 3271 AN XY: 74180

African (AFR) AF: 0.0121 AC: 501 AN: 41492

American (AMR) AF: 0.0503 AC: 763 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.0826 AC: 286 AN: 3464

East Asian (EAS) AF: 0.00370 AC: 19 AN: 5140

South Asian (SAS) AF: 0.0636 AC: 307 AN: 4826

European-Finnish (FIN) AF: 0.0282 AC: 299 AN: 10608

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0661 AC: 4480 AN: 67766

Other (OTH) AF: 0.0632 AC: 133 AN: 2106

Alfa AF: 0.0452 Hom.: 76

Bravo AF: 0.0446

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.21
DANN	Benign	0.69
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12206223; hg19: chr6-102968906;