rs6060965

Variant names:

• chr20-31818295-A-G
• rs6060965

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 0.0877 in 152,162 control chromosomes in the GnomAD database, including 660 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 0.088 (660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 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: 0.0875 AC: 13306 AN: 152044 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0268

Gnomad FIN AF: 0.0729

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.0877 AC: 13340 AN: 152162 Hom.: 660 Cov.: 32 AF XY: 0.0849 AC XY: 6317 AN XY: 74400

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0855

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0272

Gnomad4 FIN AF: 0.0729

Gnomad4 NFE AF: 0.0766

Gnomad4 OTH AF: 0.0957

Alfa AF: 0.0806 Hom.: 107

Bravo AF: 0.0902

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.71
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6060965; hg19: chr20-30406098;