rs6071822

chr20-39843516-G-Achr20-39843516-G-T

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 0.186 in 152,118 control chromosomes in the GnomAD database, including 3,095 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 0.19 (3095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.186 AC: 28302 AN: 152000 Hom.: 3093 Cov.: 32

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0898

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.186 AC: 28316 AN: 152118 Hom.: 3095 Cov.: 32 AF XY: 0.189 AC XY: 14063 AN XY: 74364

Gnomad4 AFR AF: 0.0827

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0898

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.155

Alfa AF: 0.219 Hom.: 7849

Bravo AF: 0.171

Asia WGS AF: 0.199 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.0
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6071822; hg19: chr20-38472158;