6-30900456-G-C

Variant names:

• chr6-30900456-G-C
• rs9468844

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 0.26 in 152,024 control chromosomes in the GnomAD database, including 6,047 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 0.26 (6047 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 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: 0.260 AC: 39533 AN: 151906 Hom.: 6033 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.260 AC: 39569 AN: 152024 Hom.: 6047 Cov.: 32 AF XY: 0.271 AC XY: 20104 AN XY: 74290

African (AFR) AF: 0.271 AC: 11225 AN: 41432

American (AMR) AF: 0.368 AC: 5620 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3137 AN: 5174

South Asian (SAS) AF: 0.509 AC: 2449 AN: 4810

European-Finnish (FIN) AF: 0.257 AC: 2710 AN: 10556

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12612 AN: 67982

Other (OTH) AF: 0.263 AC: 555 AN: 2108

Alfa AF: 0.110 Hom.: 205

Bravo AF: 0.266

Asia WGS AF: 0.546 AC: 1896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9468844; hg19: chr6-30868233;