rs6032619

Variant names:

• chr20-45998388-T-C
• rs6032619

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 0.925 in 152,310 control chromosomes in the GnomAD database, including 65,565 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 0.93 (65565 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140836 AN: 152190 Hom.: 65532 Cov.: 33

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.925 AC: 140914 AN: 152310 Hom.: 65565 Cov.: 33 AF XY: 0.921 AC XY: 68625 AN XY: 74478

African (AFR) AF: 0.922 AC: 38337 AN: 41564

American (AMR) AF: 0.817 AC: 12500 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3333 AN: 3472

East Asian (EAS) AF: 0.762 AC: 3941 AN: 5174

South Asian (SAS) AF: 0.861 AC: 4160 AN: 4832

European-Finnish (FIN) AF: 0.947 AC: 10064 AN: 10624

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.962 AC: 65460 AN: 68028

Other (OTH) AF: 0.914 AC: 1933 AN: 2114

Alfa AF: 0.938 Hom.: 168009

Bravo AF: 0.912

Asia WGS AF: 0.763 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.52
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs6032619; hg19: chr20-44627027;