rs1460133

Positions:

• chr4-136721193-T-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 0.106 in 152,200 control chromosomes in the GnomAD database, including 978 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 (978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.143 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: 0.106 AC: 16115 AN: 152082 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0961

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.106 AC: 16117 AN: 152200 Hom.: 978 Cov.: 32 AF XY: 0.109 AC XY: 8075 AN XY: 74402

Gnomad4 AFR AF: 0.0613

Gnomad4 AMR AF: 0.0961

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.0155

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.108

Alfa AF: 0.114 Hom.: 193

Bravo AF: 0.0956

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1460133; hg19: chr4-137642348;