chr8-143564835-G-A

Variant names:

• chr8-143564835-G-A
• rs4552913

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 0.757 in 152,220 control chromosomes in the GnomAD database, including 44,150 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 0.76 (44150 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 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: 0.757 AC: 115148 AN: 152102 Hom.: 44145 Cov.: 34

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.757 AC: 115190 AN: 152220 Hom.: 44150 Cov.: 34 AF XY: 0.766 AC XY: 57024 AN XY: 74434

African (AFR) AF: 0.625 AC: 25918 AN: 41486

American (AMR) AF: 0.808 AC: 12360 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2898 AN: 3472

East Asian (EAS) AF: 0.971 AC: 5040 AN: 5190

South Asian (SAS) AF: 0.833 AC: 4025 AN: 4832

European-Finnish (FIN) AF: 0.852 AC: 9043 AN: 10614

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53356 AN: 68012

Other (OTH) AF: 0.746 AC: 1576 AN: 2114

Alfa AF: 0.777 Hom.: 63489

Bravo AF: 0.749

Asia WGS AF: 0.857 AC: 2979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.55
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs4552913; hg19: chr8-144647005;