rs1454694

Variant names:

• chr4-181276794-T-C
• rs1454694

Your query was ambiguous. Multiple possible variants found:

• chr4-181276794-T-C
• chr4-181276794-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;