16-3906073-C-G

Variant names:

• chr16-3906073-C-G
• rs2080248

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 0.913 in 152,172 control chromosomes in the GnomAD database, including 64,301 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 0.91 (64301 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.585

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 (NFE) allele frequency at 95% confidence interval = 0.982 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: 0.914 AC: 138945 AN: 152054 Hom.: 64283 Cov.: 31

Gnomad AFR AF: 0.749

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.913 AC: 139002 AN: 152172 Hom.: 64301 Cov.: 31 AF XY: 0.916 AC XY: 68152 AN XY: 74428

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.986

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.925

Alfa AF: 0.957 Hom.: 3413

Bravo AF: 0.900

Asia WGS AF: 0.897 AC: 3120 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	2.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2080248; hg19: chr16-3956074;