rs6489847

Variant names:

• chr12-112520909-G-A
• rs6489847

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 0.209 in 151,302 control chromosomes in the GnomAD database, including 5,310 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 0.21 (5310 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.209 AC: 31543 AN: 151208 Hom.: 5312 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.209 AC: 31582 AN: 151302 Hom.: 5310 Cov.: 31 AF XY: 0.214 AC XY: 15823 AN XY: 73824

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0949

Gnomad4 OTH AF: 0.196

Alfa AF: 0.175 Hom.: 538

Bravo AF: 0.231

Asia WGS AF: 0.474 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6489847; hg19: chr12-112958713;