rs11867581

chr17-30295210-A-Gchr17-30295210-A-T

Variant summary

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

The XR_007065700.1(LOC124903971):n.521A>G 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 0.561 in 151,886 control chromosomes in the GnomAD database, including 27,214 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 0.56 (27214 hom., cov: 30)
• Consequence: LOC124903971 XR_007065700.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

LOC124903971 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903971	XR_007065700.1	n.521A>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85093 AN: 151768 Hom.: 27137 Cov.: 30

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.561 AC: 85234 AN: 151886 Hom.: 27214 Cov.: 30 AF XY: 0.556 AC XY: 41284 AN XY: 74232

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.512

Alfa AF: 0.448 Hom.: 20988

Bravo AF: 0.570

Asia WGS AF: 0.410 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.2
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11867581; hg19: chr17-28622228;