rs12359272

Variant names:

• chr10-95605406-G-A
• rs12359272

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 0.253 in 152,114 control chromosomes in the GnomAD database, including 6,337 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 0.25 (6337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 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: 0.254 AC: 38565 AN: 151996 Hom.: 6344 Cov.: 32

Gnomad AFR AF: 0.0650

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0373

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.253 AC: 38545 AN: 152114 Hom.: 6337 Cov.: 32 AF XY: 0.253 AC XY: 18804 AN XY: 74368

Gnomad4 AFR AF: 0.0648

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0368

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.235

Alfa AF: 0.301 Hom.: 1275

Bravo AF: 0.252

Asia WGS AF: 0.117 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12359272; hg19: chr10-97365163;