8-59691634-T-C

Variant names:

• chr8-59691634-T-C
• rs16925150

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0867 in 152,234 control chromosomes in the GnomAD database, including 1,402 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 0.087 (1402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

ACMG classification

Verdict is Benign. Variant got -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 = 0.24 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: 0.0865 AC: 13164 AN: 152116 Hom.: 1397 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.00623

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0867 AC: 13196 AN: 152234 Hom.: 1402 Cov.: 32 AF XY: 0.0887 AC XY: 6603 AN XY: 74460

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.0789

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.0847

Gnomad4 FIN AF: 0.00226

Gnomad4 NFE AF: 0.00623

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0170 Hom.: 170

Bravo AF: 0.0974

Asia WGS AF: 0.153 AC: 533 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	5.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16925150; hg19: chr8-60604193;