rs58926603

Variant names:

• chr17-6438550-A-G
• rs58926603
• XR_001752776.2:n.419-1213T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-6438550-A-G
• chr17-6438550-A-T

Variant summary

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

The XR_001752776.2(LOC107985017):​n.419-1213T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 (11954 hom., cov: 14)
• Consequence: LOC107985017 XR_001752776.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 2 publications found

Genes affected

LOC107985017 (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 (EAS) allele frequency at 95% confidence interval = 0.591 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: 0.475 AC: 50773 AN: 106852 Hom.: 11953 Cov.: 14

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.475 AC: 50776 AN: 106880 Hom.: 11954 Cov.: 14 AF XY: 0.482 AC XY: 23629 AN XY: 49044

African (AFR) AF: 0.577 AC: 15212 AN: 26384

American (AMR) AF: 0.443 AC: 3897 AN: 8794

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1469 AN: 3068

East Asian (EAS) AF: 0.613 AC: 2180 AN: 3558

South Asian (SAS) AF: 0.529 AC: 1580 AN: 2984

European-Finnish (FIN) AF: 0.535 AC: 1864 AN: 3486

Middle Eastern (MID) AF: 0.567 AC: 85 AN: 150

European-Non Finnish (NFE) AF: 0.419 AC: 23599 AN: 56270

Other (OTH) AF: 0.464 AC: 658 AN: 1418

Alfa AF: 0.463 Hom.: 1286

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-0.99

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: rs58926603;

hg19: chr17-6341870;

COSMIC: COSV51505823;