16-52878387-T-C

Variant names:

• chr16-52878387-T-C
• rs1344484

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 0.413 in 152,136 control chromosomes in the GnomAD database, including 13,130 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 0.41 (13130 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 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: 0.413 AC: 62754 AN: 152018 Hom.: 13108 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.413 AC: 62805 AN: 152136 Hom.: 13130 Cov.: 33 AF XY: 0.412 AC XY: 30644 AN XY: 74358

African (AFR) AF: 0.442 AC: 18349 AN: 41504

American (AMR) AF: 0.464 AC: 7093 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3470

East Asian (EAS) AF: 0.598 AC: 3089 AN: 5166

South Asian (SAS) AF: 0.405 AC: 1955 AN: 4824

European-Finnish (FIN) AF: 0.401 AC: 4235 AN: 10558

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25649 AN: 68004

Other (OTH) AF: 0.402 AC: 849 AN: 2114

Alfa AF: 0.397 Hom.: 33035

Bravo AF: 0.426

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.63
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1344484; hg19: chr16-52912299;