4-110810809-G-T

Variant names:

• chr4-110810809-G-T
• rs6533531

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 0.423 in 151,686 control chromosomes in the GnomAD database, including 16,791 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 0.42 (16791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.661
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.424 AC: 64209 AN: 151568 Hom.: 16792 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.423 AC: 64197 AN: 151686 Hom.: 16791 Cov.: 32 AF XY: 0.411 AC XY: 30469 AN XY: 74078

African (AFR) AF: 0.157 AC: 6514 AN: 41432

American (AMR) AF: 0.359 AC: 5449 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1555 AN: 3462

East Asian (EAS) AF: 0.0977 AC: 503 AN: 5146

South Asian (SAS) AF: 0.373 AC: 1794 AN: 4810

European-Finnish (FIN) AF: 0.525 AC: 5521 AN: 10520

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41175 AN: 67824

Other (OTH) AF: 0.454 AC: 956 AN: 2104

Alfa AF: 0.515 Hom.: 35274

Bravo AF: 0.399

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.28
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs6533531; hg19: chr4-111731965;