rs11885014

Positions:

• chr2-18766049-G-A
• chr2-18766049-G-C
• chr2-18766049-G-T

Variant summary

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

The XR_007086234.1(LOC105373456):​n.973+77721G>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 0.337 in 151,872 control chromosomes in the GnomAD database, including 10,229 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 0.34 (10229 hom., cov: 32)
• Consequence: LOC105373456 XR_007086234.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

Genes affected

LOC105373456 (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 = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373456	XR_007086234.1	n.973+77721G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51161 AN: 151754 Hom.: 10199 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0808

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.337 AC: 51233 AN: 151872 Hom.: 10229 Cov.: 32 AF XY: 0.331 AC XY: 24588 AN XY: 74226

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.0808

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.302

Alfa AF: 0.263 Hom.: 6831

Bravo AF: 0.348

Asia WGS AF: 0.132 AC: 460 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	4.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11885014; hg19: chr2-18947315;