rs1573638

Variant names:

• chr16-13809456-G-A
• rs1573638

Your query was ambiguous. Multiple possible variants found:

• chr16-13809456-G-A
• chr16-13809456-G-C

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 0.135 in 152,094 control chromosomes in the GnomAD database, including 2,063 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 0.14 (2063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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: 0.135 AC: 20505 AN: 151976 Hom.: 2057 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0660

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.135 AC: 20547 AN: 152094 Hom.: 2063 Cov.: 32 AF XY: 0.136 AC XY: 10089 AN XY: 74356

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0660

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0779 Hom.: 1185

Bravo AF: 0.149

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.050
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1573638; hg19: chr16-13903313;