rs6078600

Variant names:

• chr20-12456001-G-A
• rs6078600

Your query was ambiguous. Multiple possible variants found:

• chr20-12456001-G-A
• chr20-12456001-G-C
• chr20-12456001-G-T

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 0.0894 in 152,096 control chromosomes in the GnomAD database, including 713 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 0.089 (713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 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: 0.0895 AC: 13599 AN: 151978 Hom.: 713 Cov.: 32

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0773

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

GnomAD4 genome AF: 0.0894 AC: 13604 AN: 152096 Hom.: 713 Cov.: 32 AF XY: 0.0907 AC XY: 6746 AN XY: 74346

Gnomad4 AFR AF: 0.0431

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0770

Alfa AF: 0.0583 Hom.: 72

Bravo AF: 0.0872

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6078600; hg19: chr20-12436649;