rs9295873

Variant names:

• chr6-30446458-A-G
• rs9295873

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 0.164 in 152,146 control chromosomes in the GnomAD database, including 2,230 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 0.16 (2230 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 15 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 (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.164 AC: 24871 AN: 152026 Hom.: 2229 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.164 AC: 24888 AN: 152146 Hom.: 2230 Cov.: 32 AF XY: 0.159 AC XY: 11804 AN XY: 74406

African (AFR) AF: 0.241 AC: 10003 AN: 41466

American (AMR) AF: 0.106 AC: 1626 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.0309 AC: 160 AN: 5180

South Asian (SAS) AF: 0.140 AC: 676 AN: 4818

European-Finnish (FIN) AF: 0.0890 AC: 944 AN: 10610

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10530 AN: 67994

Other (OTH) AF: 0.152 AC: 322 AN: 2114

Alfa AF: 0.154 Hom.: 7008

Bravo AF: 0.171

Asia WGS AF: 0.0730 AC: 254 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	6.2
DANN	Benign	0.79
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs9295873; hg19: chr6-30414235;