rs1387243

Variant names:

• chr12-28940591-T-C
• rs1387243

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 0.21 in 151,986 control chromosomes in the GnomAD database, including 3,671 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 0.21 (3671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589

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 (NFE) allele frequency at 95% confidence interval = 0.249 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: 0.210 AC: 31960 AN: 151868 Hom.: 3671 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.210 AC: 31950 AN: 151986 Hom.: 3671 Cov.: 32 AF XY: 0.211 AC XY: 15692 AN XY: 74282

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.208

Alfa AF: 0.241 Hom.: 4689

Bravo AF: 0.200

Asia WGS AF: 0.199 AC: 691 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	6.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1387243; hg19: chr12-29093524;