rs12208888

chr6-31279653-C-T

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 0.126 in 152,210 control chromosomes in the GnomAD database, including 1,327 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 0.13 (1327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.169 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: 0.126 AC: 19192 AN: 152092 Hom.: 1327 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.126 AC: 19200 AN: 152210 Hom.: 1327 Cov.: 32 AF XY: 0.127 AC XY: 9429 AN XY: 74408

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0673

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.140

Alfa AF: 0.134 Hom.: 194

Bravo AF: 0.125

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.3
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12208888; hg19: chr6-31247430;