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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0820 AC: 3406 AN: 41518

American (AMR) AF: 0.100 AC: 1535 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2064 AN: 5168

South Asian (SAS) AF: 0.0997 AC: 480 AN: 4816

European-Finnish (FIN) AF: 0.0705 AC: 747 AN: 10596

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.0433 AC: 2943 AN: 67988

Other (OTH) AF: 0.0819 AC: 173 AN: 2112

Alfa AF: 0.0590 Hom.: 403

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
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs12571469; hg19: chr10-109201632;