rs4480754

Variant names:

• chr15-23641794-T-G
• rs4480754

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 0.277 in 151,994 control chromosomes in the GnomAD database, including 6,183 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 0.28 (6183 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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: 0.277 AC: 42028 AN: 151876 Hom.: 6186 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.277 AC: 42053 AN: 151994 Hom.: 6183 Cov.: 33 AF XY: 0.279 AC XY: 20690 AN XY: 74264

African (AFR) AF: 0.275 AC: 11402 AN: 41462

American (AMR) AF: 0.339 AC: 5184 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3472

East Asian (EAS) AF: 0.531 AC: 2728 AN: 5138

South Asian (SAS) AF: 0.266 AC: 1280 AN: 4820

European-Finnish (FIN) AF: 0.215 AC: 2270 AN: 10562

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17272 AN: 67956

Other (OTH) AF: 0.289 AC: 609 AN: 2104

Alfa AF: 0.264 Hom.: 13120

Bravo AF: 0.289

Asia WGS AF: 0.365 AC: 1265 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	0.47
DANN	Benign	0.49
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs4480754; hg19: chr15-23886941;