16-57290158-C-T

Variant names:

• chr16-57290158-C-T
• rs8044834

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 0.451 in 152,058 control chromosomes in the GnomAD database, including 18,095 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 0.45 (18095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 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: 0.452 AC: 68629 AN: 151940 Hom.: 18089 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.451 AC: 68645 AN: 152058 Hom.: 18095 Cov.: 32 AF XY: 0.459 AC XY: 34079 AN XY: 74326

African (AFR) AF: 0.162 AC: 6701 AN: 41490

American (AMR) AF: 0.524 AC: 7985 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1680 AN: 3468

East Asian (EAS) AF: 0.558 AC: 2885 AN: 5166

South Asian (SAS) AF: 0.452 AC: 2176 AN: 4818

European-Finnish (FIN) AF: 0.653 AC: 6905 AN: 10574

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38717 AN: 67980

Other (OTH) AF: 0.500 AC: 1054 AN: 2108

Alfa AF: 0.504 Hom.: 7484

Bravo AF: 0.429

Asia WGS AF: 0.517 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.66
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs8044834; hg19: chr16-57324070;