rs11867581

Variant names:

• chr17-30295210-A-G
• rs11867581
• XR_007065700.1:n.521A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-30295210-A-G
• chr17-30295210-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

LOC124903971 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124903971	XR_007065700.1	n.521A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294641	ENST00000724906.1	n.84-266A>G		intron_variant	Intron 1 of 2
ENSG00000294641	ENST00000724907.1	n.75-266A>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.882 AC: 36578 AN: 41472

American (AMR) AF: 0.481 AC: 7340 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1306 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1124 AN: 5142

South Asian (SAS) AF: 0.395 AC: 1897 AN: 4804

European-Finnish (FIN) AF: 0.489 AC: 5155 AN: 10550

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30163 AN: 67898

Other (OTH) AF: 0.512 AC: 1080 AN: 2108

Alfa AF: 0.463 Hom.: 50699

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
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs11867581; hg19: chr17-28622228;