rs6591904

Variant names:

• chr11-80731676-A-G
• rs6591904
• XR_001748502.2:n.130+3267A>G

Variant summary

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

The XR_001748502.2(LOC105369409):​n.130+3267A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,936 control chromosomes in the GnomAD database, including 17,657 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 0.48 (17657 hom., cov: 32)
• Consequence: LOC105369409 XR_001748502.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 0 publications found

Genes affected

LOC105369409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72433 AN: 151818 Hom.: 17633 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.477 AC: 72501 AN: 151936 Hom.: 17657 Cov.: 32 AF XY: 0.478 AC XY: 35449 AN XY: 74234

African (AFR) AF: 0.549 AC: 22741 AN: 41434

American (AMR) AF: 0.469 AC: 7154 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1533 AN: 5156

South Asian (SAS) AF: 0.389 AC: 1878 AN: 4822

European-Finnish (FIN) AF: 0.523 AC: 5515 AN: 10540

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30505 AN: 67940

Other (OTH) AF: 0.471 AC: 993 AN: 2110

Alfa AF: 0.463 Hom.: 2094

Bravo AF: 0.479

Asia WGS AF: 0.335 AC: 1159 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.58
PhyloP100		0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6591904;

hg19: chr11-80442719;