rs12571469

Positions:

• chr10-107441874-G-A
• chr10-107441874-G-C
• chr10-107441874-G-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 0.0764 in 152,148 control chromosomes in the GnomAD database, including 765 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 0.076 (765 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

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 (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0764 AC: 11613 AN: 152030 Hom.: 762 Cov.: 33

Gnomad AFR AF: 0.0816

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0823

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

GnomAD4 genome AF: 0.0764 AC: 11630 AN: 152148 Hom.: 765 Cov.: 33 AF XY: 0.0807 AC XY: 5999 AN XY: 74382

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.0997

Gnomad4 FIN AF: 0.0705

Gnomad4 NFE AF: 0.0433

Gnomad4 OTH AF: 0.0819

Alfa AF: 0.0572 Hom.: 294

Bravo AF: 0.0824

Asia WGS AF: 0.220 AC: 763 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	7.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12571469; hg19: chr10-109201632;