chr20-40600144-C-T

Variant names:

• chr20-40600144-C-T
• rs6102059
• XR_001754596.2:n.472-2206G>A

Variant summary

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

The XR_001754596.2(LOC102724968):​n.472-2206G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,898 control chromosomes in the GnomAD database, including 8,947 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 0.34 (8947 hom., cov: 32)
• Consequence: LOC102724968 XR_001754596.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• Publications: 55 publications found

Genes affected

LOC102724968 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.528 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: 0.336 AC: 50942 AN: 151782 Hom.: 8940 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.336 AC: 50964 AN: 151898 Hom.: 8947 Cov.: 32 AF XY: 0.335 AC XY: 24859 AN XY: 74220

African (AFR) AF: 0.415 AC: 17180 AN: 41390

American (AMR) AF: 0.261 AC: 3982 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2811 AN: 5162

South Asian (SAS) AF: 0.351 AC: 1688 AN: 4808

European-Finnish (FIN) AF: 0.272 AC: 2868 AN: 10534

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20672 AN: 67952

Other (OTH) AF: 0.300 AC: 635 AN: 2114

Alfa AF: 0.315 Hom.: 24937

Bravo AF: 0.337

Asia WGS AF: 0.411 AC: 1426 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	0.60
DANN	Benign	0.75
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6102059; hg19: chr20-39228784;