18-11972440-A-G

Variant names:

• chr18-11972440-A-G
• rs1787984

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 0.402 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 4 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 = 0.71 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.717 AC: 29743 AN: 41492

American (AMR) AF: 0.281 AC: 4301 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2121 AN: 5120

South Asian (SAS) AF: 0.452 AC: 2176 AN: 4816

European-Finnish (FIN) AF: 0.226 AC: 2392 AN: 10586

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18356 AN: 67950

Other (OTH) AF: 0.360 AC: 761 AN: 2112

Alfa AF: 0.320 Hom.: 22473

Bravo AF: 0.417

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.22
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1787984; hg19: chr18-11972439;