4-167613550-A-G

Variant names:

• chr4-167613550-A-G
• rs1518180

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 0.866 in 152,192 control chromosomes in the GnomAD database, including 57,227 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 0.87 (57227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.866 AC: 131734 AN: 152076 Hom.: 57182 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.866 AC: 131833 AN: 152192 Hom.: 57227 Cov.: 32 AF XY: 0.872 AC XY: 64860 AN XY: 74402

African (AFR) AF: 0.830 AC: 34455 AN: 41534

American (AMR) AF: 0.903 AC: 13794 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3030 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5183 AN: 5184

South Asian (SAS) AF: 0.905 AC: 4367 AN: 4826

European-Finnish (FIN) AF: 0.924 AC: 9807 AN: 10612

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58314 AN: 67974

Other (OTH) AF: 0.888 AC: 1878 AN: 2116

Alfa AF: 0.871 Hom.: 6155

Bravo AF: 0.866

Asia WGS AF: 0.961 AC: 3338 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1518180; hg19: chr4-168534701;