rs1570504

Variant names:

• chr9-108292529-C-A
• rs1570504
• XR_001746881.2:n.720+18137G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-108292529-C-A
• chr9-108292529-C-G

Variant summary

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

The XR_001746881.2(LOC105376214):​n.720+18137G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 151,984 control chromosomes in the GnomAD database, including 4,803 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 0.22 (4803 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 1 publications found

Genes affected

LOC105376214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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: 0.220 AC: 33438 AN: 151866 Hom.: 4792 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.0585

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0272

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.220 AC: 33474 AN: 151984 Hom.: 4803 Cov.: 32 AF XY: 0.220 AC XY: 16344 AN XY: 74286

African (AFR) AF: 0.404 AC: 16755 AN: 41434

American (AMR) AF: 0.196 AC: 2986 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3468

East Asian (EAS) AF: 0.0270 AC: 140 AN: 5176

South Asian (SAS) AF: 0.146 AC: 705 AN: 4824

European-Finnish (FIN) AF: 0.188 AC: 1987 AN: 10554

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9877 AN: 67960

Other (OTH) AF: 0.192 AC: 406 AN: 2110

Alfa AF: 0.158 Hom.: 3813

Bravo AF: 0.223

Asia WGS AF: 0.108 AC: 376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1570504; hg19: chr9-111054809;