rs12206223

chr6-102521031-T-C

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 0.0452 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0121

Gnomad4 AMR AF: 0.0503

Gnomad4 ASJ AF: 0.0826

Gnomad4 EAS AF: 0.00370

Gnomad4 SAS AF: 0.0636

Gnomad4 FIN AF: 0.0282

Gnomad4 NFE AF: 0.0661

Gnomad4 OTH AF: 0.0632

Alfa AF: 0.0563 Hom.: 48

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12206223; hg19: chr6-102968906;