rs4774545

Variant names:

• chr15-49767823-T-C
• rs4774545

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 0.07 in 152,212 control chromosomes in the GnomAD database, including 680 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 0.070 (680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.151 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: 0.0697 AC: 10601 AN: 152094 Hom.: 665 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0539

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0278

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0197

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0700 AC: 10657 AN: 152212 Hom.: 680 Cov.: 32 AF XY: 0.0724 AC XY: 5386 AN XY: 74428

African (AFR) AF: 0.133 AC: 5517 AN: 41532

American (AMR) AF: 0.156 AC: 2387 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.0535 AC: 277 AN: 5180

South Asian (SAS) AF: 0.123 AC: 595 AN: 4818

European-Finnish (FIN) AF: 0.0278 AC: 295 AN: 10606

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0197 AC: 1342 AN: 68010

Other (OTH) AF: 0.0652 AC: 138 AN: 2116

Alfa AF: 0.0495 Hom.: 52

Bravo AF: 0.0811

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.067
DANN	Benign	0.39
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs4774545; hg19: chr15-50060020;