5-58279878-A-G

Variant names:

• chr5-58279878-A-G
• rs40207

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 0.641 in 151,950 control chromosomes in the GnomAD database, including 31,682 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 0.64 (31682 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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: 0.641 AC: 97268 AN: 151830 Hom.: 31658 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.641 AC: 97344 AN: 151950 Hom.: 31682 Cov.: 32 AF XY: 0.636 AC XY: 47235 AN XY: 74274

African (AFR) AF: 0.527 AC: 21839 AN: 41412

American (AMR) AF: 0.723 AC: 11048 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2544 AN: 3466

East Asian (EAS) AF: 0.777 AC: 4016 AN: 5168

South Asian (SAS) AF: 0.587 AC: 2828 AN: 4818

European-Finnish (FIN) AF: 0.571 AC: 6027 AN: 10562

Middle Eastern (MID) AF: 0.736 AC: 215 AN: 292

European-Non Finnish (NFE) AF: 0.690 AC: 46863 AN: 67932

Other (OTH) AF: 0.673 AC: 1420 AN: 2110

Alfa AF: 0.661 Hom.: 14989

Bravo AF: 0.651

Asia WGS AF: 0.664 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs40207; hg19: chr5-57575705;