4-164576231-A-G

Variant names:

• chr4-164576231-A-G
• rs4145327

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 0.931 in 152,312 control chromosomes in the GnomAD database, including 66,248 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 0.93 (66248 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.958 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: 0.931 AC: 141717 AN: 152194 Hom.: 66209 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.931 AC: 141809 AN: 152312 Hom.: 66248 Cov.: 33 AF XY: 0.933 AC XY: 69518 AN XY: 74484

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.939

Alfa AF: 0.959 Hom.: 91839

Bravo AF: 0.927

Asia WGS AF: 0.917 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4145327; hg19: chr4-165497383;