18-73410989-A-G

Position:

• chr18-73410989-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 0.411 in 152,006 control chromosomes in the GnomAD database, including 14,153 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 0.41 (14153 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73410989A>G		intergenic_region
LOC105372190	XR_007066468.1	n.1180-2267T>C		intron_variant
LOC105372190	XR_007066469.1	n.1287-2267T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62357 AN: 151890 Hom.: 14138 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.411 AC: 62422 AN: 152006 Hom.: 14153 Cov.: 31 AF XY: 0.405 AC XY: 30131 AN XY: 74306

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.381

Alfa AF: 0.261 Hom.: 999

Bravo AF: 0.432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8089528; hg19: chr18-71078224;