rs4582379

Variant names:

• chr6-27164179-G-A
• rs4582379

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 0.0878 in 152,100 control chromosomes in the GnomAD database, including 1,137 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 0.088 (1137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 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: 0.0876 AC: 13314 AN: 151982 Hom.: 1126 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0511

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0189

Gnomad OTH AF: 0.0814

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

GnomAD4 genome AF: 0.0878 AC: 13349 AN: 152100 Hom.: 1137 Cov.: 32 AF XY: 0.0888 AC XY: 6604 AN XY: 74378

African (AFR) AF: 0.212 AC: 8797 AN: 41480

American (AMR) AF: 0.100 AC: 1530 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3472

East Asian (EAS) AF: 0.141 AC: 732 AN: 5180

South Asian (SAS) AF: 0.0514 AC: 247 AN: 4810

European-Finnish (FIN) AF: 0.0503 AC: 532 AN: 10582

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0189 AC: 1285 AN: 67984

Other (OTH) AF: 0.0806 AC: 170 AN: 2110

Alfa AF: 0.0549 Hom.: 181

Bravo AF: 0.0967

Asia WGS AF: 0.0960 AC: 332 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	0.52
DANN	Benign	0.14
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4582379; hg19: chr6-27131958;