rs6072343

Positions:

• chr20-41339548-G-A

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 0.121 in 152,118 control chromosomes in the GnomAD database, including 1,288 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 0.12 (1288 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41339548G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18448 AN: 152000 Hom.: 1288 Cov.: 32

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.121 AC: 18461 AN: 152118 Hom.: 1288 Cov.: 32 AF XY: 0.122 AC XY: 9075 AN XY: 74374

Gnomad4 AFR AF: 0.0898

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.0388

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.114

Alfa AF: 0.134 Hom.: 2963

Bravo AF: 0.112

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6072343; hg19: chr20-39968188;