rs9295768

Variant names:

• chr6-28241324-G-A
• rs9295768

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 0.204 in 152,066 control chromosomes in the GnomAD database, including 3,595 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 0.20 (3595 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31024 AN: 151948 Hom.: 3583 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.204 AC: 31066 AN: 152066 Hom.: 3595 Cov.: 32 AF XY: 0.197 AC XY: 14679 AN XY: 74354

African (AFR) AF: 0.305 AC: 12639 AN: 41458

American (AMR) AF: 0.180 AC: 2752 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1002 AN: 5172

South Asian (SAS) AF: 0.174 AC: 841 AN: 4828

European-Finnish (FIN) AF: 0.0954 AC: 1009 AN: 10574

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11795 AN: 67974

Other (OTH) AF: 0.182 AC: 383 AN: 2108

Alfa AF: 0.190 Hom.: 6523

Bravo AF: 0.217

Asia WGS AF: 0.164 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.24
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs9295768; hg19: chr6-28209102;