4-164576231-A-G

Variant names:

• chr4-164576231-A-G
• rs4145327

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 0.931 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.931 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

African (AFR) AF: 0.854 AC: 35460 AN: 41530

American (AMR) AF: 0.955 AC: 14613 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3338 AN: 3472

East Asian (EAS) AF: 0.882 AC: 4578 AN: 5190

South Asian (SAS) AF: 0.970 AC: 4687 AN: 4832

European-Finnish (FIN) AF: 0.974 AC: 10346 AN: 10626

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.964 AC: 65613 AN: 68040

Other (OTH) AF: 0.939 AC: 1986 AN: 2116

Alfa AF: 0.956 Hom.: 115642

Bravo AF: 0.927

Asia WGS AF: 0.917 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.40
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs4145327; hg19: chr4-165497383;