rs9466930

Variant names:

• chr6-23840904-C-G
• rs9466930

Your query was ambiguous. Multiple possible variants found:

• chr6-23840904-C-G
• chr6-23840904-C-T

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 0.717 in 152,074 control chromosomes in the GnomAD database, including 39,475 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 0.72 (39475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.910
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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: 0.717 AC: 108978 AN: 151956 Hom.: 39464 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.717 AC: 109029 AN: 152074 Hom.: 39475 Cov.: 32 AF XY: 0.717 AC XY: 53283 AN XY: 74336

African (AFR) AF: 0.633 AC: 26258 AN: 41480

American (AMR) AF: 0.671 AC: 10243 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2768 AN: 3472

East Asian (EAS) AF: 0.530 AC: 2734 AN: 5156

South Asian (SAS) AF: 0.730 AC: 3512 AN: 4810

European-Finnish (FIN) AF: 0.729 AC: 7707 AN: 10568

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.783 AC: 53253 AN: 67998

Other (OTH) AF: 0.740 AC: 1563 AN: 2112

Alfa AF: 0.746 Hom.: 5019

Bravo AF: 0.704

Asia WGS AF: 0.626 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.65
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs9466930; hg19: chr6-23841132;