chr1-12163394-G-A

Variant names:

• chr1-12163394-G-A
• rs590368

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 0.291 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0958 AC: 3979 AN: 41554

American (AMR) AF: 0.269 AC: 4105 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1618 AN: 3472

East Asian (EAS) AF: 0.293 AC: 1518 AN: 5188

South Asian (SAS) AF: 0.370 AC: 1784 AN: 4828

European-Finnish (FIN) AF: 0.326 AC: 3450 AN: 10594

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26724 AN: 67990

Other (OTH) AF: 0.340 AC: 719 AN: 2116

Alfa AF: 0.302 Hom.: 2022

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs590368; hg19: chr1-12223451;