rs4582379

Positions:

• chr6-27164179-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.0189

Gnomad4 OTH AF: 0.0806

Alfa AF: 0.0501 Hom.: 142

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4582379; hg19: chr6-27131958;