chr8-92346182-T-C

Variant names:

• chr8-92346182-T-C
• rs1125729

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 0.199 in 152,094 control chromosomes in the GnomAD database, including 3,293 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 0.20 (3293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 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: 0.199 AC: 30199 AN: 151976 Hom.: 3283 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.199 AC: 30248 AN: 152094 Hom.: 3293 Cov.: 32 AF XY: 0.203 AC XY: 15123 AN XY: 74338

African (AFR) AF: 0.164 AC: 6789 AN: 41518

American (AMR) AF: 0.269 AC: 4113 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3470

East Asian (EAS) AF: 0.486 AC: 2510 AN: 5166

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4816

European-Finnish (FIN) AF: 0.180 AC: 1899 AN: 10578

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12025 AN: 67964

Other (OTH) AF: 0.214 AC: 452 AN: 2110

Alfa AF: 0.147 Hom.: 505

Bravo AF: 0.206

Asia WGS AF: 0.362 AC: 1260 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.2
DANN	Benign	0.68
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1125729; hg19: chr8-93358410;