18-3031069-A-G

Variant names:

• chr18-3031069-A-G
• rs7232826

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 0.575 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.529

Alfa AF: 0.496 Hom.: 30624

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7232826; hg19: chr18-3031067;