rs1320925

Variant names:

• chr12-30309047-A-G
• rs1320925

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 0.262 in 151,136 control chromosomes in the GnomAD database, including 7,141 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 0.26 (7141 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 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: 0.262 AC: 39564 AN: 151022 Hom.: 7127 Cov.: 29

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.262 AC: 39622 AN: 151136 Hom.: 7141 Cov.: 29 AF XY: 0.261 AC XY: 19241 AN XY: 73794

African (AFR) AF: 0.515 AC: 21116 AN: 40972

American (AMR) AF: 0.196 AC: 2974 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 712 AN: 3462

East Asian (EAS) AF: 0.215 AC: 1098 AN: 5110

South Asian (SAS) AF: 0.259 AC: 1244 AN: 4794

European-Finnish (FIN) AF: 0.138 AC: 1444 AN: 10434

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10132 AN: 67874

Other (OTH) AF: 0.256 AC: 539 AN: 2106

Alfa AF: 0.217 Hom.: 638

Bravo AF: 0.277

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.50
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1320925; hg19: chr12-30461980;