rs6032619

Positions:

• chr20-45998388-T-C

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 0.925 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.962

Gnomad4 OTH AF: 0.914

Alfa AF: 0.944 Hom.: 63601

Bravo AF: 0.912

Asia WGS AF: 0.763 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6032619; hg19: chr20-44627027;