chr16-79666550-G-C

Variant names:

• chr16-79666550-G-C
• rs4889009

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 0.586 in 151,980 control chromosomes in the GnomAD database, including 26,618 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 0.59 (26618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 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: 0.586 AC: 89051 AN: 151862 Hom.: 26605 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.586 AC: 89097 AN: 151980 Hom.: 26618 Cov.: 32 AF XY: 0.591 AC XY: 43929 AN XY: 74288

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.592

Alfa AF: 0.467 Hom.: 1280

Bravo AF: 0.577

Asia WGS AF: 0.517 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4889009; hg19: chr16-79700447;