8-58505103-A-T

Variant names:

• chr8-58505103-A-T
• rs7833904

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 0.547 in 152,070 control chromosomes in the GnomAD database, including 23,226 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 0.55 (23226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.643 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: 0.547 AC: 83094 AN: 151952 Hom.: 23213 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.547 AC: 83139 AN: 152070 Hom.: 23226 Cov.: 32 AF XY: 0.545 AC XY: 40495 AN XY: 74334

African (AFR) AF: 0.447 AC: 18533 AN: 41486

American (AMR) AF: 0.653 AC: 9989 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3466

East Asian (EAS) AF: 0.393 AC: 2027 AN: 5162

South Asian (SAS) AF: 0.515 AC: 2488 AN: 4828

European-Finnish (FIN) AF: 0.555 AC: 5865 AN: 10564

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.592 AC: 40238 AN: 67962

Other (OTH) AF: 0.562 AC: 1187 AN: 2112

Alfa AF: 0.556 Hom.: 2929

Bravo AF: 0.551

Asia WGS AF: 0.463 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.55
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7833904; hg19: chr8-59417662;