16-81438629-T-C

Variant names:

• chr16-81438629-T-C
• rs2098753

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 0.298 in 151,996 control chromosomes in the GnomAD database, including 6,753 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 0.30 (6753 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.298 AC: 45302 AN: 151876 Hom.: 6741 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.298 AC: 45344 AN: 151996 Hom.: 6753 Cov.: 31 AF XY: 0.299 AC XY: 22187 AN XY: 74288

African (AFR) AF: 0.283 AC: 11736 AN: 41458

American (AMR) AF: 0.243 AC: 3715 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2098 AN: 5150

South Asian (SAS) AF: 0.350 AC: 1689 AN: 4824

European-Finnish (FIN) AF: 0.301 AC: 3176 AN: 10554

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.307 AC: 20868 AN: 67960

Other (OTH) AF: 0.313 AC: 659 AN: 2106

Alfa AF: 0.293 Hom.: 5486

Bravo AF: 0.291

Asia WGS AF: 0.322 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.38
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2098753; hg19: chr16-81472234;