4-154517187-A-G

Variant names:

• chr4-154517187-A-G
• rs4235247

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 0.835 in 152,188 control chromosomes in the GnomAD database, including 53,656 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 0.84 (53656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.835 AC: 127017 AN: 152070 Hom.: 53615 Cov.: 32

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.835 AC: 127115 AN: 152188 Hom.: 53656 Cov.: 32 AF XY: 0.831 AC XY: 61837 AN XY: 74402

African (AFR) AF: 0.915 AC: 38008 AN: 41540

American (AMR) AF: 0.814 AC: 12446 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2968 AN: 3472

East Asian (EAS) AF: 0.491 AC: 2539 AN: 5170

South Asian (SAS) AF: 0.831 AC: 4005 AN: 4822

European-Finnish (FIN) AF: 0.793 AC: 8379 AN: 10562

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56076 AN: 68004

Other (OTH) AF: 0.848 AC: 1795 AN: 2116

Alfa AF: 0.829 Hom.: 146588

Bravo AF: 0.836

Asia WGS AF: 0.700 AC: 2436 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	0.77
DANN	Benign	0.25
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4235247; hg19: chr4-155438339;