rs9469457

Variant names:

• chr6-33522105-G-A
• rs9469457
• XR_001743876.1:n.18-2614C>T

Variant summary

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

The XR_001743876.1(LOC107986537):​n.18-2614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,224 control chromosomes in the GnomAD database, including 265 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 0.038 (265 hom., cov: 32)
• Consequence: LOC107986537 XR_001743876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 5 publications found

Genes affected

LOC107986537 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 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: 0.0384 AC: 5842 AN: 152106 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00878

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0385 AC: 5858 AN: 152224 Hom.: 265 Cov.: 32 AF XY: 0.0382 AC XY: 2847 AN XY: 74442

African (AFR) AF: 0.110 AC: 4585 AN: 41528

American (AMR) AF: 0.0225 AC: 344 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3468

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5174

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4816

European-Finnish (FIN) AF: 0.00198 AC: 21 AN: 10622

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00878 AC: 597 AN: 68002

Other (OTH) AF: 0.0345 AC: 73 AN: 2114

Alfa AF: 0.0218 Hom.: 187

Bravo AF: 0.0442

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.61
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9469457; hg19: chr6-33489882;