rs16912145

Variant names:

• chr10-58322908-G-A
• rs16912145

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 0.191 in 152,030 control chromosomes in the GnomAD database, including 4,041 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 0.19 (4041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.191 AC: 29047 AN: 151912 Hom.: 4026 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.191 AC: 29101 AN: 152030 Hom.: 4041 Cov.: 32 AF XY: 0.192 AC XY: 14251 AN XY: 74322

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0823

Gnomad4 NFE AF: 0.0926

Gnomad4 OTH AF: 0.173

Alfa AF: 0.113 Hom.: 2043

Bravo AF: 0.208

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16912145; hg19: chr10-60082668;