rs1389504

chr16-17840448-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.737 in 151,814 control chromosomes in the GnomAD database, including 42,075 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 0.74 (42075 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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: 0.737 AC: 111766 AN: 151698 Hom.: 42019 Cov.: 30

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.737 AC: 111880 AN: 151814 Hom.: 42075 Cov.: 30 AF XY: 0.737 AC XY: 54696 AN XY: 74166

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.753

Alfa AF: 0.673 Hom.: 40859

Bravo AF: 0.748

Asia WGS AF: 0.775 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
Cadd	Benign	18
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1389504; hg19: chr16-17934305;