rs12571469

Variant names:

• chr10-107441874-G-A
• rs12571469

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;