rs6060965

chr20-31818295-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;