16-65796106-T-C

Variant names:

• chr16-65796106-T-C
• rs468905

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 0.778 in 152,048 control chromosomes in the GnomAD database, including 46,749 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 0.78 (46749 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.64
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.778 AC: 118197 AN: 151930 Hom.: 46691 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.778 AC: 118324 AN: 152048 Hom.: 46749 Cov.: 31 AF XY: 0.783 AC XY: 58155 AN XY: 74314

African (AFR) AF: 0.900 AC: 37349 AN: 41508

American (AMR) AF: 0.771 AC: 11782 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2547 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5130 AN: 5152

South Asian (SAS) AF: 0.808 AC: 3891 AN: 4818

European-Finnish (FIN) AF: 0.748 AC: 7902 AN: 10558

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47223 AN: 67948

Other (OTH) AF: 0.769 AC: 1625 AN: 2112

Alfa AF: 0.761 Hom.: 6263

Bravo AF: 0.784

Asia WGS AF: 0.905 AC: 3146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.92
DANN	Benign	0.28
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs468905; hg19: chr16-65830009;