16-46634557-G-T

Position:

• chr16-46634557-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0217 in 151,602 control chromosomes in the GnomAD database, including 49 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 0.022 (49 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0217 (3290/151602) while in subpopulation NFE AF= 0.0348 (2366/67918). AF 95% confidence interval is 0.0337. There are 49 homozygotes in gnomad4. There are 1528 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 49 gene

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: 0.0218 AC: 3295 AN: 151486 Hom.: 50 Cov.: 31

Gnomad AFR AF: 0.00548

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0137

Gnomad ASJ AF: 0.00838

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00915

Gnomad FIN AF: 0.0310

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0226

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

GnomAD4 genome AF: 0.0217 AC: 3290 AN: 151602 Hom.: 49 Cov.: 31 AF XY: 0.0206 AC XY: 1528 AN XY: 74044

Gnomad4 AFR AF: 0.00547

Gnomad4 AMR AF: 0.0137

Gnomad4 ASJ AF: 0.00838

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.00895

Gnomad4 FIN AF: 0.0310

Gnomad4 NFE AF: 0.0348

Gnomad4 OTH AF: 0.0219

Alfa AF: 0.0199 Hom.: 7

Bravo AF: 0.0204

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56168099; hg19: chr16-46668469;