17-37685518-A-G

Position:

• chr17-37685518-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 0.202 in 152,102 control chromosomes in the GnomAD database, including 3,261 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 0.20 (3261 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

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 (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37685518A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30641 AN: 151984 Hom.: 3252 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.202 AC: 30676 AN: 152102 Hom.: 3261 Cov.: 32 AF XY: 0.207 AC XY: 15426 AN XY: 74376

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.224

Alfa AF: 0.192 Hom.: 4313

Bravo AF: 0.197

Asia WGS AF: 0.344 AC: 1193 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	7.4
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: rs11263755; hg19: chr17-36045521;