rs1920790

Variant names:

• chr12-91099011-A-C
• rs1920790

Your query was ambiguous. Multiple possible variants found:

• chr12-91099011-A-C
• chr12-91099011-A-G
• chr12-91099011-A-T

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 0.167 in 152,148 control chromosomes in the GnomAD database, including 2,561 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 0.17 (2561 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 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: 0.167 AC: 25314 AN: 152030 Hom.: 2556 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0863

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.167 AC: 25341 AN: 152148 Hom.: 2561 Cov.: 33 AF XY: 0.161 AC XY: 11945 AN XY: 74416

African (AFR) AF: 0.283 AC: 11724 AN: 41482

American (AMR) AF: 0.136 AC: 2079 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3466

East Asian (EAS) AF: 0.0557 AC: 289 AN: 5188

South Asian (SAS) AF: 0.0560 AC: 270 AN: 4822

European-Finnish (FIN) AF: 0.0863 AC: 916 AN: 10610

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8908 AN: 68000

Other (OTH) AF: 0.163 AC: 345 AN: 2114

Alfa AF: 0.0754 Hom.: 109

Bravo AF: 0.177

Asia WGS AF: 0.0670 AC: 234 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.44
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs1920790; hg19: chr12-91492788;