rs1445732

Variant names:

• chr5-13121785-A-G
• rs1445732

Your query was ambiguous. Multiple possible variants found:

• chr5-13121785-A-G
• chr5-13121785-A-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 0.0252 in 152,182 control chromosomes in the GnomAD database, including 248 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 0.025 (248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.84

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 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: 0.0252 AC: 3834 AN: 152064 Hom.: 249 Cov.: 32

Gnomad AFR AF: 0.00413

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0252 AC: 3830 AN: 152182 Hom.: 248 Cov.: 32 AF XY: 0.0291 AC XY: 2167 AN XY: 74380

Gnomad4 AFR AF: 0.00411

Gnomad4 AMR AF: 0.0260

Gnomad4 ASJ AF: 0.00547

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.0427

Gnomad4 FIN AF: 0.0742

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.0148 Hom.: 4

Bravo AF: 0.0225

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1445732; hg19: chr5-13121897;