20-40600144-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC102724968 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724968	XR_001754596.2	n.472-2206G>A		intron_variant	Intron 5 of 7
LOC102724968	XR_001754597.1	n.409-2206G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.300

Alfa AF: 0.311 Hom.: 9394

Bravo AF: 0.337

Asia WGS AF: 0.411 AC: 1426 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	0.60
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6102059; hg19: chr20-39228784;