rs1873104

Variant names:

• chr8-58758209-G-A
• rs1873104

Your query was ambiguous. Multiple possible variants found:

• chr8-58758209-G-A
• chr8-58758209-G-C
• chr8-58758209-G-T

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 0.692 in 152,142 control chromosomes in the GnomAD database, including 37,296 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 0.69 (37296 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 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: 0.692 AC: 105194 AN: 152024 Hom.: 37250 Cov.: 33

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.692 AC: 105288 AN: 152142 Hom.: 37296 Cov.: 33 AF XY: 0.688 AC XY: 51126 AN XY: 74362

African (AFR) AF: 0.856 AC: 35552 AN: 41518

American (AMR) AF: 0.626 AC: 9564 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2262 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3402 AN: 5180

South Asian (SAS) AF: 0.602 AC: 2902 AN: 4820

European-Finnish (FIN) AF: 0.571 AC: 6038 AN: 10580

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43350 AN: 67976

Other (OTH) AF: 0.701 AC: 1476 AN: 2106

Alfa AF: 0.638 Hom.: 21301

Bravo AF: 0.705

Asia WGS AF: 0.605 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.54
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1873104; hg19: chr8-59670768;