rs6589377

Variant names:

• chr11-113485014-G-A
• rs6589377
• XR_948024.2:n.378+5388C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-113485014-G-A
• chr11-113485014-G-C
• chr11-113485014-G-T

Variant summary

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

The XR_948024.2(LOC105369501):​n.378+5388C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,122 control chromosomes in the GnomAD database, including 40,072 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 0.72 (40072 hom., cov: 32)
• Consequence: LOC105369501 XR_948024.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 21 publications found

Genes affected

LOC105369501 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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: 0.719 AC: 109239 AN: 152004 Hom.: 40010 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.719 AC: 109364 AN: 152122 Hom.: 40072 Cov.: 32 AF XY: 0.729 AC XY: 54238 AN XY: 74362

African (AFR) AF: 0.824 AC: 34199 AN: 41520

American (AMR) AF: 0.683 AC: 10428 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1960 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5040 AN: 5176

South Asian (SAS) AF: 0.757 AC: 3640 AN: 4808

European-Finnish (FIN) AF: 0.823 AC: 8716 AN: 10588

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43147 AN: 67976

Other (OTH) AF: 0.659 AC: 1386 AN: 2104

Alfa AF: 0.648 Hom.: 135444

Bravo AF: 0.709

Asia WGS AF: 0.867 AC: 3011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.68
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs6589377; hg19: chr11-113355736;