rs4566595

Variant names:

• chr4-4904055-C-A
• rs4566595

Your query was ambiguous. Multiple possible variants found:

• chr4-4904055-C-A
• chr4-4904055-C-G

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 0.7 in 152,112 control chromosomes in the GnomAD database, including 37,788 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 0.70 (37788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.815 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: 0.699 AC: 106300 AN: 151994 Hom.: 37726 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.700 AC: 106417 AN: 152112 Hom.: 37788 Cov.: 32 AF XY: 0.705 AC XY: 52461 AN XY: 74368

African (AFR) AF: 0.823 AC: 34148 AN: 41506

American (AMR) AF: 0.692 AC: 10591 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2388 AN: 3472

East Asian (EAS) AF: 0.715 AC: 3695 AN: 5168

South Asian (SAS) AF: 0.693 AC: 3341 AN: 4822

European-Finnish (FIN) AF: 0.733 AC: 7753 AN: 10576

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42435 AN: 67956

Other (OTH) AF: 0.686 AC: 1443 AN: 2104

Alfa AF: 0.641 Hom.: 54010

Bravo AF: 0.698

Asia WGS AF: 0.707 AC: 2461 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	0.56
DANN	Benign	0.65
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4566595; hg19: chr4-4905782;