chr8-113873203-G-A

Variant names:

• chr8-113873203-G-A
• rs6469488

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 0.912 in 152,256 control chromosomes in the GnomAD database, including 63,879 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 0.91 (63879 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.97 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: 0.912 AC: 138756 AN: 152138 Hom.: 63838 Cov.: 31

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.912 AC: 138852 AN: 152256 Hom.: 63879 Cov.: 31 AF XY: 0.908 AC XY: 67577 AN XY: 74444

African (AFR) AF: 0.978 AC: 40672 AN: 41580

American (AMR) AF: 0.795 AC: 12140 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3286 AN: 3472

East Asian (EAS) AF: 0.598 AC: 3090 AN: 5164

South Asian (SAS) AF: 0.945 AC: 4555 AN: 4820

European-Finnish (FIN) AF: 0.883 AC: 9358 AN: 10598

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62761 AN: 68030

Other (OTH) AF: 0.901 AC: 1902 AN: 2110

Alfa AF: 0.914 Hom.: 106918

Bravo AF: 0.900

Asia WGS AF: 0.794 AC: 2763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.50
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs6469488; hg19: chr8-114885432;