chr16-9135920-G-A

Position:

• chr16-9135920-G-A

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 0.345 in 152,084 control chromosomes in the GnomAD database, including 14,543 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 0.35 (14543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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 (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52373 AN: 151966 Hom.: 14489 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.345 AC: 52490 AN: 152084 Hom.: 14543 Cov.: 32 AF XY: 0.344 AC XY: 25578 AN XY: 74342

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.294

Alfa AF: 0.181 Hom.: 4979

Bravo AF: 0.382

Asia WGS AF: 0.276 AC: 958 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	2.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8050335; hg19: chr16-9229777;