rs4285184

Variant names:

• chr5-180779656-A-G
• rs4285184

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 0.403 in 152,046 control chromosomes in the GnomAD database, including 15,629 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 0.40 (15629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 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: 0.402 AC: 61148 AN: 151928 Hom.: 15579 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.403 AC: 61257 AN: 152046 Hom.: 15629 Cov.: 32 AF XY: 0.400 AC XY: 29736 AN XY: 74338

African (AFR) AF: 0.723 AC: 29990 AN: 41456

American (AMR) AF: 0.341 AC: 5211 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 917 AN: 3472

East Asian (EAS) AF: 0.403 AC: 2084 AN: 5166

South Asian (SAS) AF: 0.489 AC: 2360 AN: 4830

European-Finnish (FIN) AF: 0.237 AC: 2504 AN: 10560

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17069 AN: 67974

Other (OTH) AF: 0.376 AC: 792 AN: 2106

Alfa AF: 0.361 Hom.: 1632

Bravo AF: 0.421

Asia WGS AF: 0.464 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs4285184; hg19: chr5-180206656;