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. The variant received -12 ACMG points: 0P and 12B.

Score: -12 - Benign

-12

BP4_StrongBA1

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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.518 AC: 21473 AN: 41454

American (AMR) AF: 0.596 AC: 9106 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2037 AN: 3468

East Asian (EAS) AF: 0.901 AC: 4650 AN: 5160

South Asian (SAS) AF: 0.593 AC: 2855 AN: 4814

European-Finnish (FIN) AF: 0.671 AC: 7087 AN: 10568

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37317 AN: 67944

Other (OTH) AF: 0.571 AC: 1206 AN: 2112

Alfa AF: 0.551 Hom.: 41052

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

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