chr20-11872507-A-G

Position:

• chr20-11872507-A-G

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 0.417 in 152,004 control chromosomes in the GnomAD database, including 13,335 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 0.42 (13335 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

Genes affected

(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 = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11872507A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00687	ENST00000427835.3	n.186-314T>C		intron_variant		3
LINC00687	ENST00000656506.1	n.119-1780T>C		intron_variant
LINC00687	ENST00000666572.1	n.177-314T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63375 AN: 151886 Hom.: 13325 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.417 AC: 63409 AN: 152004 Hom.: 13335 Cov.: 32 AF XY: 0.414 AC XY: 30746 AN XY: 74284

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.409

Alfa AF: 0.391 Hom.: 5229

Bravo AF: 0.412

Asia WGS AF: 0.337 AC: 1171 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	0.91
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs803880; hg19: chr20-11853155;