16-181542-C-T

Variant names:

• chr16-181542-C-T
• rs1203834

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 0.0579 in 152,332 control chromosomes in the GnomAD database, including 335 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 0.058 (335 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 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: 0.0580 AC: 8826 AN: 152214 Hom.: 335 Cov.: 34

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0437

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0579 AC: 8821 AN: 152332 Hom.: 335 Cov.: 34 AF XY: 0.0592 AC XY: 4412 AN XY: 74486

African (AFR) AF: 0.0184 AC: 764 AN: 41586

American (AMR) AF: 0.0436 AC: 667 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3472

East Asian (EAS) AF: 0.127 AC: 659 AN: 5170

South Asian (SAS) AF: 0.120 AC: 580 AN: 4828

European-Finnish (FIN) AF: 0.0844 AC: 897 AN: 10628

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0718 AC: 4886 AN: 68022

Other (OTH) AF: 0.0652 AC: 138 AN: 2116

Alfa AF: 0.0292 Hom.: 24

Bravo AF: 0.0527

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.70
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1203834; hg19: chr16-231541;