rs4285153

Variant names:

• chr4-110857577-A-G
• rs4285153

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 0.715 in 151,966 control chromosomes in the GnomAD database, including 40,009 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 0.71 (40009 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.715 AC: 108617 AN: 151848 Hom.: 40002 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.715 AC: 108654 AN: 151966 Hom.: 40009 Cov.: 31 AF XY: 0.724 AC XY: 53779 AN XY: 74288

African (AFR) AF: 0.524 AC: 21673 AN: 41398

American (AMR) AF: 0.771 AC: 11751 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2774 AN: 3470

East Asian (EAS) AF: 0.835 AC: 4314 AN: 5164

South Asian (SAS) AF: 0.831 AC: 4010 AN: 4824

European-Finnish (FIN) AF: 0.846 AC: 8945 AN: 10576

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.776 AC: 52752 AN: 67976

Other (OTH) AF: 0.712 AC: 1502 AN: 2110

Alfa AF: 0.753 Hom.: 9727

Bravo AF: 0.701

Asia WGS AF: 0.788 AC: 2733 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.76
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs4285153; hg19: chr4-111778733;