rs6070706

Variant names:

• chr20-59053184-C-T
• rs6070706

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 0.115 in 152,124 control chromosomes in the GnomAD database, including 1,232 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 0.11 (1232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 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: 0.115 AC: 17432 AN: 152006 Hom.: 1233 Cov.: 32

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.115 AC: 17425 AN: 152124 Hom.: 1232 Cov.: 32 AF XY: 0.120 AC XY: 8915 AN XY: 74360

Gnomad4 AFR AF: 0.0610

Gnomad4 AMR AF: 0.0892

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.0651

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.0991

Alfa AF: 0.128 Hom.: 1740

Bravo AF: 0.0992

Asia WGS AF: 0.0490 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6070706; hg19: chr20-57628239;