20-1439202-C-T

Position:

• chr20-1439202-C-T

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 0.0702 in 152,228 control chromosomes in the GnomAD database, including 425 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 0.070 (425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 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: 0.0702 AC: 10673 AN: 152110 Hom.: 424 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0708

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0328

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0702 AC: 10691 AN: 152228 Hom.: 425 Cov.: 32 AF XY: 0.0677 AC XY: 5039 AN XY: 74440

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0707

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0431

Gnomad4 FIN AF: 0.0328

Gnomad4 NFE AF: 0.0631

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0631 Hom.: 387

Bravo AF: 0.0736

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485823; hg19: chr20-1419846;