4-179210306-G-C

Variant names:

• chr4-179210306-G-C
• rs9312245

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 0.96 in 152,168 control chromosomes in the GnomAD database, including 70,351 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 0.96 (70351 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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: 0.960 AC: 146027 AN: 152050 Hom.: 70309 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.982

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.953

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.969

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

GnomAD4 genome AF: 0.960 AC: 146128 AN: 152168 Hom.: 70351 Cov.: 31 AF XY: 0.961 AC XY: 71483 AN XY: 74390

African (AFR) AF: 0.878 AC: 36440 AN: 41488

American (AMR) AF: 0.982 AC: 14980 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3418 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5149 AN: 5178

South Asian (SAS) AF: 0.953 AC: 4584 AN: 4810

European-Finnish (FIN) AF: 1.00 AC: 10606 AN: 10610

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67737 AN: 68028

Other (OTH) AF: 0.968 AC: 2048 AN: 2116

Alfa AF: 0.977 Hom.: 9032

Bravo AF: 0.956

Asia WGS AF: 0.945 AC: 3287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.051
DANN	Benign	0.42
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs9312245; hg19: chr4-180131460;