rs6489992

Variant names:

• chr12-114914964-G-A
• rs6489992

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.477 AC: 19775 AN: 41478

American (AMR) AF: 0.323 AC: 4928 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1714 AN: 3468

East Asian (EAS) AF: 0.169 AC: 872 AN: 5174

South Asian (SAS) AF: 0.378 AC: 1821 AN: 4820

European-Finnish (FIN) AF: 0.359 AC: 3795 AN: 10568

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24832 AN: 67958

Other (OTH) AF: 0.389 AC: 821 AN: 2108

Alfa AF: 0.400 Hom.: 5401

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6489992; hg19: chr12-115352769;