rs1567499

Positions:

• chr4-66557425-A-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.0712

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.00819

Gnomad4 NFE AF: 0.00922

Gnomad4 OTH AF: 0.0945

Alfa AF: 0.0671 Hom.: 177

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567499; hg19: chr4-67423143;