chr8-59511329-T-C

Variant names:

• chr8-59511329-T-C
• rs10504292

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 0.0212 in 152,236 control chromosomes in the GnomAD database, including 86 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 0.021 (86 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.117 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: 0.0211 AC: 3209 AN: 152118 Hom.: 85 Cov.: 31

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0215

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.00969

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00628

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0212 AC: 3221 AN: 152236 Hom.: 86 Cov.: 31 AF XY: 0.0228 AC XY: 1698 AN XY: 74430

African (AFR) AF: 0.0335 AC: 1393 AN: 41550

American (AMR) AF: 0.0214 AC: 327 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.125 AC: 649 AN: 5174

South Asian (SAS) AF: 0.0469 AC: 226 AN: 4822

European-Finnish (FIN) AF: 0.00969 AC: 103 AN: 10626

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00628 AC: 427 AN: 68014

Other (OTH) AF: 0.0185 AC: 39 AN: 2112

Alfa AF: 0.0138 Hom.: 64

Bravo AF: 0.0216

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.51
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10504292; hg19: chr8-60423888;