rs6018428

Positions:

• chr20-37423192-G-A
• chr20-37423192-G-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 0.291 in 152,030 control chromosomes in the GnomAD database, including 8,964 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 0.29 (8964 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37423192G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44176 AN: 151912 Hom.: 8941 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.291 AC: 44259 AN: 152030 Hom.: 8964 Cov.: 32 AF XY: 0.284 AC XY: 21117 AN XY: 74298

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.0994

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.266

Alfa AF: 0.200 Hom.: 2333

Bravo AF: 0.315

Asia WGS AF: 0.238 AC: 828 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6018428; hg19: chr20-36051595;