rs7271186

Variant names:

• chr20-39229452-G-A
• rs7271186

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;