rs484171

Variant names:

• chr11-102860672-A-G
• rs484171
• XR_007062868.1:n.1992-4526A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-102860672-A-G
• chr11-102860672-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062868.1(LOC124902741):​n.1992-4526A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 151,950 control chromosomes in the GnomAD database, including 1,352 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 0.11 (1352 hom., cov: 32)
• Consequence: LOC124902741 XR_007062868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 5 publications found

Genes affected

LOC124902741 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16511 AN: 151832 Hom.: 1347 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0989

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.109 AC: 16517 AN: 151950 Hom.: 1352 Cov.: 32 AF XY: 0.107 AC XY: 7922 AN XY: 74284

African (AFR) AF: 0.229 AC: 9491 AN: 41468

American (AMR) AF: 0.0742 AC: 1133 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3472

East Asian (EAS) AF: 0.110 AC: 568 AN: 5182

South Asian (SAS) AF: 0.0978 AC: 470 AN: 4808

European-Finnish (FIN) AF: 0.0407 AC: 428 AN: 10516

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.0529 AC: 3596 AN: 67932

Other (OTH) AF: 0.112 AC: 235 AN: 2106

Alfa AF: 0.0800 Hom.: 99

Bravo AF: 0.116

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.39
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs484171; hg19: chr11-102731403;