rs6076960

Variant names:

• chr20-6205510-A-C
• rs6076960

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;