chr16-31387145-T-C

Position:

• chr16-31387145-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.134 in 152,228 control chromosomes in the GnomAD database, including 1,545 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 0.13 (1545 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20359 AN: 152110 Hom.: 1549 Cov.: 33

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.134 AC: 20357 AN: 152228 Hom.: 1545 Cov.: 33 AF XY: 0.133 AC XY: 9927 AN XY: 74440

Gnomad4 AFR AF: 0.0834

Gnomad4 AMR AF: 0.0895

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0407

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.123

Alfa AF: 0.153 Hom.: 1845

Bravo AF: 0.122

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17708876; hg19: chr16-31398466;