rs306604

Variant names:

• chr12-27503832-G-A
• rs306604

Your query was ambiguous. Multiple possible variants found:

• chr12-27503832-G-A
• chr12-27503832-G-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 0.108 in 152,092 control chromosomes in the GnomAD database, including 1,742 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 0.11 (1742 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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: 0.107 AC: 16315 AN: 151974 Hom.: 1729 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0586

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0356

Gnomad OTH AF: 0.0801

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

GnomAD4 genome AF: 0.108 AC: 16363 AN: 152092 Hom.: 1742 Cov.: 33 AF XY: 0.108 AC XY: 8012 AN XY: 74362

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.0586

Gnomad4 ASJ AF: 0.0427

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0569

Gnomad4 FIN AF: 0.0296

Gnomad4 NFE AF: 0.0356

Gnomad4 OTH AF: 0.0802

Alfa AF: 0.0723 Hom.: 127

Bravo AF: 0.117

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs306604; hg19: chr12-27656765;