rs12515716

Variant names:

• chr5-89893319-G-A
• rs12515716

Your query was ambiguous. Multiple possible variants found:

• chr5-89893319-G-A
• chr5-89893319-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 0.122 in 151,986 control chromosomes in the GnomAD database, including 1,344 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 0.12 (1344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 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: 0.122 AC: 18525 AN: 151870 Hom.: 1341 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.122 AC: 18535 AN: 151986 Hom.: 1344 Cov.: 32 AF XY: 0.123 AC XY: 9109 AN XY: 74296

Gnomad4 AFR AF: 0.0825

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.157

Alfa AF: 0.112 Hom.: 134

Bravo AF: 0.130

Asia WGS AF: 0.146 AC: 508 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12515716; hg19: chr5-89189136;