rs6076960

Positions:

• chr20-6205510-A-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 0.472 in 151,918 control chromosomes in the GnomAD database, including 17,396 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 0.47 (17396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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: 0.472 AC: 71666 AN: 151800 Hom.: 17385 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.472 AC: 71714 AN: 151918 Hom.: 17396 Cov.: 32 AF XY: 0.469 AC XY: 34803 AN XY: 74214

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.493

Alfa AF: 0.505 Hom.: 6502

Bravo AF: 0.456

Asia WGS AF: 0.334 AC: 1157 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6076960; hg19: chr20-6186157;