rs6012770

Variant names:

• chr20-37675713-G-A
• rs6012770

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0939 in 152,208 control chromosomes in the GnomAD database, including 921 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 0.094 (921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.910
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14278 AN: 152090 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0773

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.0939 AC: 14292 AN: 152208 Hom.: 921 Cov.: 32 AF XY: 0.0926 AC XY: 6890 AN XY: 74430

African (AFR) AF: 0.172 AC: 7137 AN: 41492

American (AMR) AF: 0.0730 AC: 1116 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.0291 AC: 151 AN: 5188

South Asian (SAS) AF: 0.0321 AC: 155 AN: 4822

European-Finnish (FIN) AF: 0.0773 AC: 820 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4359 AN: 68012

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.0743 Hom.: 627

Bravo AF: 0.0973

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.43
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs6012770; hg19: chr20-36304115;