20-17844499-T-C

Position:

• chr20-17844499-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 0.396 in 151,304 control chromosomes in the GnomAD database, including 12,757 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 0.40 (12757 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17844499T>C		intergenic_region
LOC107985440	XR_001754511.2	n.226+5666A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.396 AC: 59855 AN: 151186 Hom.: 12747 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.396 AC: 59889 AN: 151304 Hom.: 12757 Cov.: 31 AF XY: 0.392 AC XY: 28993 AN XY: 73966

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.359

Alfa AF: 0.339 Hom.: 12440

Bravo AF: 0.412

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077147; hg19: chr20-17825143;