rs1389504

Variant names:

• chr16-17840448-A-C
• rs1389504

Your query was ambiguous. Multiple possible variants found:

• chr16-17840448-A-C
• chr16-17840448-A-G
• chr16-17840448-A-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;