rs12661230

Variant names:

• chr6-89825748-A-G
• rs12661230

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 0.277 in 152,000 control chromosomes in the GnomAD database, including 5,928 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 0.28 (5928 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 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: 0.277 AC: 42013 AN: 151882 Hom.: 5922 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.277 AC: 42033 AN: 152000 Hom.: 5928 Cov.: 32 AF XY: 0.277 AC XY: 20602 AN XY: 74288

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.265

Alfa AF: 0.294 Hom.: 3622

Bravo AF: 0.269

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12661230; hg19: chr6-90535467;