chr16-77983154-C-T

Variant names:

• chr16-77983154-C-T
• rs430046

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 0.377 in 151,830 control chromosomes in the GnomAD database, including 11,120 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 0.38 (11120 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900
• Publications: 18 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 (AMR) allele frequency at 95% confidence interval = 0.403 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: 0.378 AC: 57282 AN: 151710 Hom.: 11108 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.377 AC: 57312 AN: 151830 Hom.: 11120 Cov.: 31 AF XY: 0.376 AC XY: 27866 AN XY: 74202

African (AFR) AF: 0.320 AC: 13262 AN: 41440

American (AMR) AF: 0.409 AC: 6241 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1493 AN: 3462

East Asian (EAS) AF: 0.334 AC: 1719 AN: 5146

South Asian (SAS) AF: 0.362 AC: 1740 AN: 4810

European-Finnish (FIN) AF: 0.360 AC: 3797 AN: 10534

Middle Eastern (MID) AF: 0.431 AC: 125 AN: 290

European-Non Finnish (NFE) AF: 0.407 AC: 27659 AN: 67884

Other (OTH) AF: 0.417 AC: 878 AN: 2106

Alfa AF: 0.401 Hom.: 31545

Bravo AF: 0.379

Asia WGS AF: 0.361 AC: 1256 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	0.96
DANN	Benign	0.69
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs430046; hg19: chr16-78017051;