chr16-3888601-T-A

Variant names:

• chr16-3888601-T-A
• rs2386817

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 0.848 in 152,144 control chromosomes in the GnomAD database, including 57,409 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 0.85 (57409 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129047 AN: 152026 Hom.: 57399 Cov.: 31

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.848 AC: 129084 AN: 152144 Hom.: 57409 Cov.: 31 AF XY: 0.851 AC XY: 63295 AN XY: 74380

African (AFR) AF: 0.557 AC: 23085 AN: 41454

American (AMR) AF: 0.923 AC: 14104 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3156 AN: 3470

East Asian (EAS) AF: 0.781 AC: 4028 AN: 5158

South Asian (SAS) AF: 0.873 AC: 4211 AN: 4826

European-Finnish (FIN) AF: 0.995 AC: 10572 AN: 10620

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.984 AC: 66943 AN: 68022

Other (OTH) AF: 0.868 AC: 1827 AN: 2104

Alfa AF: 0.906 Hom.: 7990

Bravo AF: 0.830

Asia WGS AF: 0.803 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.80
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2386817; hg19: chr16-3938602;