rs720131

Variant names:

• chr8-116903776-G-A
• rs720131

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 0.409 in 151,882 control chromosomes in the GnomAD database, including 14,433 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 0.41 (14433 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 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: 0.409 AC: 62075 AN: 151764 Hom.: 14409 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.343

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.409 AC: 62158 AN: 151882 Hom.: 14433 Cov.: 31 AF XY: 0.409 AC XY: 30325 AN XY: 74214

African (AFR) AF: 0.611 AC: 25316 AN: 41416

American (AMR) AF: 0.453 AC: 6918 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1601 AN: 3466

East Asian (EAS) AF: 0.631 AC: 3249 AN: 5148

South Asian (SAS) AF: 0.303 AC: 1460 AN: 4814

European-Finnish (FIN) AF: 0.251 AC: 2646 AN: 10536

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19796 AN: 67926

Other (OTH) AF: 0.387 AC: 813 AN: 2100

Alfa AF: 0.317 Hom.: 6950

Bravo AF: 0.435

Asia WGS AF: 0.459 AC: 1593 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	0.041
DANN	Benign	0.70
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs720131; hg19: chr8-117916015;