rs1454694

chr4-181276794-T-Cchr4-181276794-T-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 0.197 in 152,096 control chromosomes in the GnomAD database, including 3,174 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 0.20 (3174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 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: 0.197 AC: 29884 AN: 151978 Hom.: 3172 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.197 AC: 29890 AN: 152096 Hom.: 3174 Cov.: 32 AF XY: 0.197 AC XY: 14682 AN XY: 74344

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.198

Alfa AF: 0.220 Hom.: 5094

Bravo AF: 0.184

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.6
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1454694; hg19: chr4-182197947;