rs12257945

Variant names:

• chr10-36818072-G-A
• rs12257945

Your query was ambiguous. Multiple possible variants found:

• chr10-36818072-G-A
• chr10-36818072-G-C
• chr10-36818072-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 0.487 in 152,106 control chromosomes in the GnomAD database, including 18,428 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 0.49 (18428 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 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: 0.487 AC: 73984 AN: 151988 Hom.: 18411 Cov.: 33

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.487 AC: 74027 AN: 152106 Hom.: 18428 Cov.: 33 AF XY: 0.491 AC XY: 36514 AN XY: 74340

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.479

Alfa AF: 0.454 Hom.: 25506

Bravo AF: 0.491

Asia WGS AF: 0.690 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12257945; hg19: chr10-37107000;