4-186088818-T-C

Variant names:

• chr4-186088818-T-C
• rs4862633

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 0.769 in 152,174 control chromosomes in the GnomAD database, including 45,261 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 0.77 (45261 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 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: 0.769 AC: 116961 AN: 152054 Hom.: 45234 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.769 AC: 117038 AN: 152174 Hom.: 45261 Cov.: 33 AF XY: 0.775 AC XY: 57649 AN XY: 74396

African (AFR) AF: 0.749 AC: 31084 AN: 41506

American (AMR) AF: 0.822 AC: 12569 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2092 AN: 3468

East Asian (EAS) AF: 0.881 AC: 4547 AN: 5162

South Asian (SAS) AF: 0.721 AC: 3481 AN: 4826

European-Finnish (FIN) AF: 0.865 AC: 9167 AN: 10598

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51624 AN: 68000

Other (OTH) AF: 0.755 AC: 1597 AN: 2114

Alfa AF: 0.757 Hom.: 117801

Bravo AF: 0.767

Asia WGS AF: 0.801 AC: 2784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs4862633; hg19: chr4-187009972;