rs6489992

Variant names:

• chr12-114914964-G-A
• rs6489992

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 0.388 in 152,058 control chromosomes in the GnomAD database, including 11,931 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 0.39 (11931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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: 0.388 AC: 58952 AN: 151936 Hom.: 11914 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.388 AC: 59009 AN: 152058 Hom.: 11931 Cov.: 32 AF XY: 0.383 AC XY: 28502 AN XY: 74324

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.389

Alfa AF: 0.365 Hom.: 1898

Bravo AF: 0.390

Asia WGS AF: 0.300 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6489992; hg19: chr12-115352769;