rs6054631

chr20-6961773-T-C

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 0.289 in 152,158 control chromosomes in the GnomAD database, including 7,168 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 0.29 (7168 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

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 (AFR) allele frequency at 95% confidence interval = 0.439 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: 0.288 AC: 43808 AN: 152040 Hom.: 7138 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.289 AC: 43904 AN: 152158 Hom.: 7168 Cov.: 33 AF XY: 0.286 AC XY: 21255 AN XY: 74390

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.259

Alfa AF: 0.240 Hom.: 9550

Bravo AF: 0.290

Asia WGS AF: 0.286 AC: 999 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	1.5
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: rs6054631; hg19: chr20-6942420;