16-29777142-C-T

Variant names:

• chr16-29777142-C-T
• rs235657

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 0.891 in 149,478 control chromosomes in the GnomAD database, including 61,270 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 0.89 (61270 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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: 0.891 AC: 133153 AN: 149374 Hom.: 61250 Cov.: 25

Gnomad AFR AF: 0.632

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.996

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.891 AC: 133215 AN: 149478 Hom.: 61270 Cov.: 25 AF XY: 0.893 AC XY: 64866 AN XY: 72612

African (AFR) AF: 0.632 AC: 25580 AN: 40466

American (AMR) AF: 0.952 AC: 14057 AN: 14764

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3416 AN: 3468

East Asian (EAS) AF: 0.936 AC: 4706 AN: 5028

South Asian (SAS) AF: 0.997 AC: 4773 AN: 4788

European-Finnish (FIN) AF: 1.00 AC: 9828 AN: 9828

Middle Eastern (MID) AF: 0.955 AC: 277 AN: 290

European-Non Finnish (NFE) AF: 0.998 AC: 67722 AN: 67842

Other (OTH) AF: 0.929 AC: 1944 AN: 2092

Alfa AF: 0.933 Hom.: 6944

Bravo AF: 0.874

Asia WGS AF: 0.953 AC: 3315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.48
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs235657; hg19: chr16-29788463;