20-17817862-A-G

Position:

• chr20-17817862-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001754511.2(LOC107985440):​n.337-1429T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,988 control chromosomes in the GnomAD database, including 38,994 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 0.70 (38994 hom., cov: 30)
• Consequence: LOC107985440 XR_001754511.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983

Genes affected

LOC107985440 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985440	XR_001754511.2	n.337-1429T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106585 AN: 151870 Hom.: 38932 Cov.: 30

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.702 AC: 106701 AN: 151988 Hom.: 38994 Cov.: 30 AF XY: 0.703 AC XY: 52229 AN XY: 74294

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.685

Alfa AF: 0.588 Hom.: 5448

Bravo AF: 0.717

Asia WGS AF: 0.698 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs241141; hg19: chr20-17798507;