16-57385374-C-T

Variant names:

• chr16-57385374-C-T
• rs614230

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 0.609 in 152,096 control chromosomes in the GnomAD database, including 28,439 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 0.61 (28439 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.638 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: 0.609 AC: 92564 AN: 151978 Hom.: 28421 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.609 AC: 92632 AN: 152096 Hom.: 28439 Cov.: 32 AF XY: 0.607 AC XY: 45105 AN XY: 74346

African (AFR) AF: 0.554 AC: 23001 AN: 41496

American (AMR) AF: 0.587 AC: 8962 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2284 AN: 3470

East Asian (EAS) AF: 0.610 AC: 3150 AN: 5168

South Asian (SAS) AF: 0.454 AC: 2187 AN: 4822

European-Finnish (FIN) AF: 0.695 AC: 7347 AN: 10576

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43708 AN: 67974

Other (OTH) AF: 0.616 AC: 1302 AN: 2112

Alfa AF: 0.629 Hom.: 49217

Bravo AF: 0.603

Asia WGS AF: 0.490 AC: 1702 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	0.55
DANN	Benign	0.40
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs614230; hg19: chr16-57419286;