4-189602787-C-G

Variant names:

• chr4-189602787-C-G
• rs3911167

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 0.785 in 152,138 control chromosomes in the GnomAD database, including 47,032 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 0.79 (47032 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.785 AC: 119360 AN: 152020 Hom.: 46996 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.785 AC: 119448 AN: 152138 Hom.: 47032 Cov.: 32 AF XY: 0.789 AC XY: 58673 AN XY: 74348

African (AFR) AF: 0.819 AC: 33971 AN: 41488

American (AMR) AF: 0.792 AC: 12124 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2389 AN: 3468

East Asian (EAS) AF: 0.846 AC: 4373 AN: 5168

South Asian (SAS) AF: 0.739 AC: 3559 AN: 4814

European-Finnish (FIN) AF: 0.845 AC: 8950 AN: 10590

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.761 AC: 51715 AN: 67990

Other (OTH) AF: 0.732 AC: 1548 AN: 2116

Alfa AF: 0.784 Hom.: 5828

Bravo AF: 0.785

Asia WGS AF: 0.803 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.26
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs3911167; hg19: chr4-190523941;