18-3031069-A-G

Variant names:

• chr18-3031069-A-G
• rs7232826

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 0.575 in 151,880 control chromosomes in the GnomAD database, including 27,141 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 0.58 (27141 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 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: 0.575 AC: 87280 AN: 151762 Hom.: 27094 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.575 AC: 87382 AN: 151880 Hom.: 27141 Cov.: 31 AF XY: 0.571 AC XY: 42385 AN XY: 74208

African (AFR) AF: 0.832 AC: 34503 AN: 41452

American (AMR) AF: 0.447 AC: 6818 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1465 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1631 AN: 5148

South Asian (SAS) AF: 0.423 AC: 2036 AN: 4810

European-Finnish (FIN) AF: 0.497 AC: 5213 AN: 10494

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33962 AN: 67956

Other (OTH) AF: 0.529 AC: 1110 AN: 2100

Alfa AF: 0.516 Hom.: 78199

Bravo AF: 0.579

Asia WGS AF: 0.395 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.57
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs7232826; hg19: chr18-3031067;