rs3859048

chr16-57366674-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00926

Gnomad4 AMR AF: 0.0495

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.0300

Gnomad4 FIN AF: 0.0337

Gnomad4 NFE AF: 0.0127

Gnomad4 OTH AF: 0.0303

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3859048; hg19: chr16-57400586;