rs9725312

Variant names:

• chr1-244875516-C-A
• rs9725312
• XM_047439568.1:c.217-10785G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-244875516-C-A
• chr1-244875516-C-G
• chr1-244875516-C-T

Variant summary

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

The XM_047439568.1(LOC124904588):​c.217-10785G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,102 control chromosomes in the GnomAD database, including 10,312 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 0.24 (10312 hom., cov: 32)
• Consequence: LOC124904588 XM_047439568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 5 publications found

Genes affected

LOC124904588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 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: 0.237 AC: 36064 AN: 151984 Hom.: 10270 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.238 AC: 36154 AN: 152102 Hom.: 10312 Cov.: 32 AF XY: 0.235 AC XY: 17478 AN XY: 74374

African (AFR) AF: 0.686 AC: 28459 AN: 41460

American (AMR) AF: 0.107 AC: 1639 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0528 AC: 183 AN: 3466

East Asian (EAS) AF: 0.176 AC: 910 AN: 5174

South Asian (SAS) AF: 0.105 AC: 507 AN: 4820

European-Finnish (FIN) AF: 0.0790 AC: 837 AN: 10592

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0468 AC: 3184 AN: 68006

Other (OTH) AF: 0.180 AC: 380 AN: 2110

Alfa AF: 0.126 Hom.: 8141

Bravo AF: 0.258

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.54
DANN	Benign	0.36
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs9725312; hg19: chr1-245038818;