rs1567499

Variant names:

• chr4-66557425-A-C
• rs1567499

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 0.107 in 152,206 control chromosomes in the GnomAD database, including 2,471 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 0.11 (2471 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 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: 0.107 AC: 16225 AN: 152088 Hom.: 2459 Cov.: 33

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.00819

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00922

Gnomad OTH AF: 0.0955

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

GnomAD4 genome AF: 0.107 AC: 16269 AN: 152206 Hom.: 2471 Cov.: 33 AF XY: 0.103 AC XY: 7680 AN XY: 74440

African (AFR) AF: 0.338 AC: 14017 AN: 41474

American (AMR) AF: 0.0712 AC: 1088 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 116 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4828

European-Finnish (FIN) AF: 0.00819 AC: 87 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00922 AC: 627 AN: 68024

Other (OTH) AF: 0.0945 AC: 200 AN: 2116

Alfa AF: 0.0769 Hom.: 223

Bravo AF: 0.121

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.2
DANN	Benign	0.79
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs1567499; hg19: chr4-67423143;