18-37697659-T-C

Position:

• chr18-37697659-T-C

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 0.0506 in 152,304 control chromosomes in the GnomAD database, including 495 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 0.051 (495 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37697659T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285940	ENST00000649194.1	n.111-28185T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7707 AN: 152186 Hom.: 492 Cov.: 33

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0438

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0506 AC: 7712 AN: 152304 Hom.: 495 Cov.: 33 AF XY: 0.0534 AC XY: 3976 AN XY: 74472

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.0844

Gnomad4 NFE AF: 0.0438

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0488 Hom.: 74

Bravo AF: 0.0614

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.15
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2042762; hg19: chr18-35277622;