rs12022410

Variant names:

• chr1-65688250-A-G
• rs12022410

Your query was ambiguous. Multiple possible variants found:

• chr1-65688250-A-G
• chr1-65688250-A-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 0.567 in 151,990 control chromosomes in the GnomAD database, including 24,984 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 0.57 (24984 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.567 AC: 86125 AN: 151872 Hom.: 24933 Cov.: 31

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.567 AC: 86239 AN: 151990 Hom.: 24984 Cov.: 31 AF XY: 0.575 AC XY: 42712 AN XY: 74274

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.571

Alfa AF: 0.551 Hom.: 30029

Bravo AF: 0.558

Asia WGS AF: 0.745 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12022410; hg19: chr1-66153933; COSMIC: COSV59950600;