4-186093998-G-C

Variant names:

• chr4-186093998-G-C
• rs1914926

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 0.799 in 152,186 control chromosomes in the GnomAD database, including 48,842 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 0.80 (48842 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 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: 0.799 AC: 121501 AN: 152068 Hom.: 48796 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.799 AC: 121604 AN: 152186 Hom.: 48842 Cov.: 32 AF XY: 0.804 AC XY: 59846 AN XY: 74402

African (AFR) AF: 0.833 AC: 34587 AN: 41524

American (AMR) AF: 0.835 AC: 12766 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2278 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4571 AN: 5172

South Asian (SAS) AF: 0.716 AC: 3452 AN: 4824

European-Finnish (FIN) AF: 0.876 AC: 9280 AN: 10588

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52096 AN: 67998

Other (OTH) AF: 0.775 AC: 1633 AN: 2108

Alfa AF: 0.728 Hom.: 2236

Bravo AF: 0.799

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.17
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs1914926; hg19: chr4-187015152;