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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369409	XR_001748502.2	n.130+3267A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs6591904; hg19: chr11-80442719;