rs13133845

Positions:

• chr4-94673465-A-G

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 0.0963 in 152,270 control chromosomes in the GnomAD database, including 746 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 0.096 (746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14661 AN: 152152 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0772

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0963 AC: 14661 AN: 152270 Hom.: 746 Cov.: 32 AF XY: 0.0946 AC XY: 7042 AN XY: 74450

Gnomad4 AFR AF: 0.0771

Gnomad4 AMR AF: 0.0699

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0401

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0998

Alfa AF: 0.112 Hom.: 809

Bravo AF: 0.0920

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13133845; hg19: chr4-95594616;