chr18-11972440-A-G

Position:

• chr18-11972440-A-G

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 0.402 in 152,028 control chromosomes in the GnomAD database, including 15,479 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 0.40 (15479 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

Genes affected

(HGNC:):

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 = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11972440A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60982 AN: 151910 Hom.: 15433 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.402 AC: 61077 AN: 152028 Hom.: 15479 Cov.: 32 AF XY: 0.399 AC XY: 29637 AN XY: 74314

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.360

Alfa AF: 0.286 Hom.: 9971

Bravo AF: 0.417

Asia WGS AF: 0.460 AC: 1598 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	0.90
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1787984; hg19: chr18-11972439;