rs4774780

Variant names:

• chr15-55538078-A-C
• rs4774780

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 0.656 in 152,032 control chromosomes in the GnomAD database, including 33,805 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 0.66 (33805 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.744 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: 0.656 AC: 99661 AN: 151916 Hom.: 33805 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.656 AC: 99701 AN: 152032 Hom.: 33805 Cov.: 32 AF XY: 0.654 AC XY: 48563 AN XY: 74308

African (AFR) AF: 0.472 AC: 19579 AN: 41444

American (AMR) AF: 0.707 AC: 10814 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2466 AN: 3470

East Asian (EAS) AF: 0.652 AC: 3381 AN: 5182

South Asian (SAS) AF: 0.636 AC: 3065 AN: 4820

European-Finnish (FIN) AF: 0.691 AC: 7283 AN: 10534

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.749 AC: 50942 AN: 67978

Other (OTH) AF: 0.656 AC: 1386 AN: 2112

Alfa AF: 0.697 Hom.: 51559

Bravo AF: 0.654

Asia WGS AF: 0.587 AC: 2041 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.39
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs4774780; hg19: chr15-55830276;