rs9921518

Variant names:

• chr16-54460512-A-G
• rs9921518

Your query was ambiguous. Multiple possible variants found:

• chr16-54460512-A-G
• chr16-54460512-A-T

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 0.767 in 152,192 control chromosomes in the GnomAD database, including 44,974 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 0.77 (44974 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 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: 0.767 AC: 116616 AN: 152074 Hom.: 44944 Cov.: 33

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.767 AC: 116696 AN: 152192 Hom.: 44974 Cov.: 33 AF XY: 0.773 AC XY: 57533 AN XY: 74402

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.764

Alfa AF: 0.774 Hom.: 61836

Bravo AF: 0.758

Asia WGS AF: 0.855 AC: 2971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.052
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9921518; hg19: chr16-54494424;