rs4463047

Variant names:

• chr4-154574381-T-C
• rs4463047

Your query was ambiguous. Multiple possible variants found:

• chr4-154574381-T-C
• chr4-154574381-T-G

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 0.157 in 151,164 control chromosomes in the GnomAD database, including 2,138 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 0.16 (2138 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 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: 0.157 AC: 23754 AN: 151066 Hom.: 2140 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0960

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.157 AC: 23751 AN: 151164 Hom.: 2138 Cov.: 31 AF XY: 0.162 AC XY: 11983 AN XY: 73830

African (AFR) AF: 0.152 AC: 6293 AN: 41312

American (AMR) AF: 0.175 AC: 2647 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2239 AN: 5120

South Asian (SAS) AF: 0.230 AC: 1100 AN: 4776

European-Finnish (FIN) AF: 0.167 AC: 1705 AN: 10182

Middle Eastern (MID) AF: 0.139 AC: 40 AN: 288

European-Non Finnish (NFE) AF: 0.132 AC: 8937 AN: 67848

Other (OTH) AF: 0.154 AC: 324 AN: 2098

Alfa AF: 0.143 Hom.: 5483

Bravo AF: 0.159

Asia WGS AF: 0.287 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.60
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4463047; hg19: chr4-155495533;