rs7271186

Positions:

• chr20-39229452-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 0.0604 in 152,244 control chromosomes in the GnomAD database, including 386 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 0.060 (386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0605 AC: 9197 AN: 152126 Hom.: 385 Cov.: 32

Gnomad AFR AF: 0.0251

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0604 AC: 9199 AN: 152244 Hom.: 386 Cov.: 32 AF XY: 0.0641 AC XY: 4770 AN XY: 74436

Gnomad4 AFR AF: 0.0250

Gnomad4 AMR AF: 0.0507

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0224

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.0714

Gnomad4 OTH AF: 0.0565

Alfa AF: 0.0707 Hom.: 592

Bravo AF: 0.0521

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7271186; hg19: chr20-37858095;