rs6579884

Variant names:

• chr5-151656737-A-G
• rs6579884

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 0.179 in 152,142 control chromosomes in the GnomAD database, including 4,512 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 0.18 (4512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 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: 0.178 AC: 27111 AN: 152024 Hom.: 4490 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.0643

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0872

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.179 AC: 27179 AN: 152142 Hom.: 4512 Cov.: 32 AF XY: 0.177 AC XY: 13138 AN XY: 74392

African (AFR) AF: 0.444 AC: 18399 AN: 41440

American (AMR) AF: 0.0918 AC: 1404 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3470

East Asian (EAS) AF: 0.0638 AC: 331 AN: 5186

South Asian (SAS) AF: 0.139 AC: 668 AN: 4812

European-Finnish (FIN) AF: 0.0872 AC: 925 AN: 10612

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0703 AC: 4780 AN: 68010

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.165 Hom.: 781

Bravo AF: 0.190

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.14
DANN	Benign	0.30
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6579884; hg19: chr5-151036298;