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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724906.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294641	ENST00000724906.1		n.84-266A>G		intron	N/A
	ENSG00000294641	ENST00000724907.1		n.75-266A>G		intron	N/A

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 v4.9

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;