4-45569697-A-G

Variant names:

• chr4-45569697-A-G
• rs840187

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 0.891 in 152,196 control chromosomes in the GnomAD database, including 60,492 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 0.89 (60492 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.891 AC: 135476 AN: 152078 Hom.: 60459 Cov.: 33

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.891 AC: 135565 AN: 152196 Hom.: 60492 Cov.: 33 AF XY: 0.893 AC XY: 66452 AN XY: 74412

African (AFR) AF: 0.829 AC: 34413 AN: 41504

American (AMR) AF: 0.931 AC: 14244 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3030 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5181 AN: 5188

South Asian (SAS) AF: 0.917 AC: 4423 AN: 4822

European-Finnish (FIN) AF: 0.924 AC: 9794 AN: 10596

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61477 AN: 68000

Other (OTH) AF: 0.895 AC: 1890 AN: 2112

Alfa AF: 0.896 Hom.: 7442

Bravo AF: 0.890

Asia WGS AF: 0.958 AC: 3329 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.64
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs840187; hg19: chr4-45571714;