4-167613550-A-G

Position:

• chr4-167613550-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;