4-181276794-T-C

Variant names:

• chr4-181276794-T-C
• rs1454694

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.125 AC: 5200 AN: 41516

American (AMR) AF: 0.153 AC: 2344 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1106 AN: 5160

South Asian (SAS) AF: 0.177 AC: 853 AN: 4812

European-Finnish (FIN) AF: 0.292 AC: 3079 AN: 10554

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15889 AN: 67990

Other (OTH) AF: 0.198 AC: 417 AN: 2106

Alfa AF: 0.217 Hom.: 6299

Bravo AF: 0.184

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.77
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs1454694; hg19: chr4-182197947;