rs590368

Variant names:

• chr1-12163394-G-A
• rs590368

Your query was ambiguous. Multiple possible variants found:

• chr1-12163394-G-A
• chr1-12163394-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 0.291 in 152,236 control chromosomes in the GnomAD database, including 7,754 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 0.29 (7754 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 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: 0.291 AC: 44256 AN: 152118 Hom.: 7759 Cov.: 33

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.291 AC: 44243 AN: 152236 Hom.: 7754 Cov.: 33 AF XY: 0.289 AC XY: 21497 AN XY: 74442

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.340

Alfa AF: 0.306 Hom.: 2016

Bravo AF: 0.281

Asia WGS AF: 0.293 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.010
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs590368; hg19: chr1-12223451;