4-79879911-G-C

Variant names:

• chr4-79879911-G-C
• rs11730315

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 0.754 in 151,960 control chromosomes in the GnomAD database, including 44,026 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 0.75 (44026 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114467 AN: 151842 Hom.: 44001 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.754 AC: 114538 AN: 151960 Hom.: 44026 Cov.: 32 AF XY: 0.745 AC XY: 55277 AN XY: 74234

African (AFR) AF: 0.744 AC: 30856 AN: 41456

American (AMR) AF: 0.642 AC: 9772 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2555 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1823 AN: 5114

South Asian (SAS) AF: 0.522 AC: 2513 AN: 4818

European-Finnish (FIN) AF: 0.844 AC: 8937 AN: 10586

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55560 AN: 67970

Other (OTH) AF: 0.732 AC: 1546 AN: 2112

Alfa AF: 0.792 Hom.: 5644

Bravo AF: 0.738

Asia WGS AF: 0.497 AC: 1731 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	1.5
DANN	Benign	0.37
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs11730315; hg19: chr4-80801065;