rs6018348

Positions:

• chr20-37409071-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 0.107 in 152,126 control chromosomes in the GnomAD database, including 2,088 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 0.11 (2088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.652

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 = 0.295 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16188 AN: 152008 Hom.: 2083 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0182

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.107 AC: 16210 AN: 152126 Hom.: 2088 Cov.: 32 AF XY: 0.105 AC XY: 7815 AN XY: 74370

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.0147

Gnomad4 NFE AF: 0.0182

Gnomad4 OTH AF: 0.0929

Alfa AF: 0.0937 Hom.: 276

Bravo AF: 0.118

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6018348; hg19: chr20-36037474;