rs3859048

Variant names:

• chr16-57366674-C-T
• rs3859048

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 0.024 in 152,336 control chromosomes in the GnomAD database, including 149 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 0.024 (149 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 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: 0.0240 AC: 3658 AN: 152218 Hom.: 149 Cov.: 33

Gnomad AFR AF: 0.00926

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0126

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0240 AC: 3651 AN: 152336 Hom.: 149 Cov.: 33 AF XY: 0.0263 AC XY: 1957 AN XY: 74490

African (AFR) AF: 0.00926 AC: 385 AN: 41578

American (AMR) AF: 0.0495 AC: 758 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00778 AC: 27 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1034 AN: 5182

South Asian (SAS) AF: 0.0300 AC: 145 AN: 4830

European-Finnish (FIN) AF: 0.0337 AC: 358 AN: 10616

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0127 AC: 861 AN: 68030

Other (OTH) AF: 0.0303 AC: 64 AN: 2114

Alfa AF: 0.0159 Hom.: 7

Bravo AF: 0.0269

Asia WGS AF: 0.103 AC: 358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.3
DANN	Benign	0.82
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs3859048; hg19: chr16-57400586;