16-82617112-A-T

Variant names:

• chr16-82617112-A-T
• rs3865188

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 0.439 in 152,034 control chromosomes in the GnomAD database, including 15,166 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 0.44 (15166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 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: 0.439 AC: 66767 AN: 151916 Hom.: 15160 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.439 AC: 66801 AN: 152034 Hom.: 15166 Cov.: 32 AF XY: 0.441 AC XY: 32795 AN XY: 74330

African (AFR) AF: 0.374 AC: 15497 AN: 41458

American (AMR) AF: 0.339 AC: 5181 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3468

East Asian (EAS) AF: 0.335 AC: 1733 AN: 5166

South Asian (SAS) AF: 0.441 AC: 2125 AN: 4822

European-Finnish (FIN) AF: 0.566 AC: 5976 AN: 10552

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33335 AN: 67964

Other (OTH) AF: 0.416 AC: 879 AN: 2114

Alfa AF: 0.453 Hom.: 8337

Bravo AF: 0.414

Asia WGS AF: 0.381 AC: 1325 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs3865188; hg19: chr16-82650717;