4-167613550-A-G

Variant names:

• chr4-167613550-A-G
• rs1518180

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.866 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

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.924

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.888

Alfa AF: 0.874 Hom.: 5882

Bravo AF: 0.866

Asia WGS AF: 0.961 AC: 3338 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1518180; hg19: chr4-168534701;