chr6-153913732-G-C

Variant names:

• chr6-153913732-G-C
• rs6900489

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 0.805 in 151,496 control chromosomes in the GnomAD database, including 49,466 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 0.80 (49466 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.75
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.805 AC: 121829 AN: 151378 Hom.: 49422 Cov.: 28

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.805 AC: 121928 AN: 151496 Hom.: 49466 Cov.: 28 AF XY: 0.806 AC XY: 59679 AN XY: 74002

African (AFR) AF: 0.904 AC: 37371 AN: 41326

American (AMR) AF: 0.867 AC: 13197 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2640 AN: 3458

East Asian (EAS) AF: 0.819 AC: 4224 AN: 5158

South Asian (SAS) AF: 0.803 AC: 3837 AN: 4780

European-Finnish (FIN) AF: 0.737 AC: 7685 AN: 10424

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50277 AN: 67826

Other (OTH) AF: 0.820 AC: 1720 AN: 2098

Alfa AF: 0.645 Hom.: 1733

Bravo AF: 0.820

Asia WGS AF: 0.811 AC: 2810 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.10
DANN	Benign	0.23
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs6900489; hg19: chr6-154234867;