rs11907114

chr20-55853891-G-A

Variant summary

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

The XR_001754724.1(LOC105372678):n.130-815G>A 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 0.332 in 151,966 control chromosomes in the GnomAD database, including 8,696 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 0.33 (8696 hom., cov: 32)
• Consequence: LOC105372678 XR_001754724.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

Genes affected

LOC105372678 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372678	XR_001754724.1	n.130-815G>A		intron_variant, non_coding_transcript_variant
LOC105372678	XR_001754723.1	n.130-815G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50374 AN: 151848 Hom.: 8695 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.332 AC: 50399 AN: 151966 Hom.: 8696 Cov.: 32 AF XY: 0.332 AC XY: 24677 AN XY: 74272

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.338

Alfa AF: 0.329 Hom.: 17027

Bravo AF: 0.325

Asia WGS AF: 0.227 AC: 785 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.14
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11907114; hg19: chr20-54428947;