rs1099399

Variant names:

• chr12-127868130-C-A
• rs1099399

Your query was ambiguous. Multiple possible variants found:

• chr12-127868130-C-A
• chr12-127868130-C-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 0.0303 in 152,044 control chromosomes in the GnomAD database, including 169 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 0.030 (169 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.091 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: 0.0302 AC: 4581 AN: 151928 Hom.: 169 Cov.: 31

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.00252

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.00537

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00475

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0303 AC: 4604 AN: 152044 Hom.: 169 Cov.: 31 AF XY: 0.0297 AC XY: 2211 AN XY: 74340

Gnomad4 AFR AF: 0.0934

Gnomad4 AMR AF: 0.0117

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.00252

Gnomad4 SAS AF: 0.0156

Gnomad4 FIN AF: 0.00537

Gnomad4 NFE AF: 0.00475

Gnomad4 OTH AF: 0.0209

Alfa AF: 0.000255 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1099399; hg19: chr12-128352675;