chr8-58505783-T-G

Variant names:

• chr8-58505783-T-G
• rs3903445

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 0.543 in 152,158 control chromosomes in the GnomAD database, including 22,959 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 0.54 (22959 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.641 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: 0.543 AC: 82588 AN: 152038 Hom.: 22943 Cov.: 33

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.543 AC: 82635 AN: 152158 Hom.: 22959 Cov.: 33 AF XY: 0.542 AC XY: 40312 AN XY: 74390

African (AFR) AF: 0.434 AC: 18032 AN: 41514

American (AMR) AF: 0.652 AC: 9967 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2122 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2033 AN: 5176

South Asian (SAS) AF: 0.515 AC: 2489 AN: 4832

European-Finnish (FIN) AF: 0.556 AC: 5878 AN: 10574

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40245 AN: 67994

Other (OTH) AF: 0.558 AC: 1178 AN: 2110

Alfa AF: 0.577 Hom.: 32431

Bravo AF: 0.547

Asia WGS AF: 0.464 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.82
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs3903445; hg19: chr8-59418342;