16-8989510-T-C

Variant names:

• chr16-8989510-T-C
• rs9927946

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 0.377 in 151,834 control chromosomes in the GnomAD database, including 12,072 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 0.38 (12072 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 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: 0.377 AC: 57178 AN: 151716 Hom.: 12070 Cov.: 30

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.377 AC: 57197 AN: 151834 Hom.: 12072 Cov.: 30 AF XY: 0.383 AC XY: 28409 AN XY: 74172

African (AFR) AF: 0.178 AC: 7385 AN: 41460

American (AMR) AF: 0.472 AC: 7170 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3472

East Asian (EAS) AF: 0.550 AC: 2813 AN: 5118

South Asian (SAS) AF: 0.433 AC: 2084 AN: 4814

European-Finnish (FIN) AF: 0.513 AC: 5391 AN: 10510

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29805 AN: 67946

Other (OTH) AF: 0.398 AC: 840 AN: 2112

Alfa AF: 0.417 Hom.: 52729

Bravo AF: 0.365

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.63
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9927946; hg19: chr16-9083367;