rs11584885

Positions:

• chr1-1164057-G-A

Variant summary

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

The XR_007065348.1(LOC124903818):​n.805G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,084 control chromosomes in the GnomAD database, including 4,381 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 0.22 (4381 hom., cov: 32)
• Consequence: LOC124903818 XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

LOC124903818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903818	XR_007065348.1	n.805G>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34008 AN: 151966 Hom.: 4382 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.224 AC: 34023 AN: 152084 Hom.: 4381 Cov.: 32 AF XY: 0.223 AC XY: 16552 AN XY: 74326

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0296

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.202

Alfa AF: 0.263 Hom.: 1107

Bravo AF: 0.205

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11584885; hg19: chr1-1099437;