4-187800358-C-A

Variant names:

• chr4-187800358-C-A
• rs4470690

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 0.718 in 152,082 control chromosomes in the GnomAD database, including 39,498 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 0.72 (39498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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: 0.718 AC: 109110 AN: 151964 Hom.: 39454 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.718 AC: 109209 AN: 152082 Hom.: 39498 Cov.: 32 AF XY: 0.725 AC XY: 53904 AN XY: 74340

African (AFR) AF: 0.677 AC: 28076 AN: 41472

American (AMR) AF: 0.744 AC: 11355 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3468

East Asian (EAS) AF: 0.889 AC: 4583 AN: 5158

South Asian (SAS) AF: 0.709 AC: 3418 AN: 4822

European-Finnish (FIN) AF: 0.796 AC: 8413 AN: 10568

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48712 AN: 68012

Other (OTH) AF: 0.709 AC: 1497 AN: 2112

Alfa AF: 0.708 Hom.: 46350

Bravo AF: 0.716

Asia WGS AF: 0.820 AC: 2855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.28
DANN	Benign	0.90
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4470690; hg19: chr4-188721512;