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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904588	XM_047439568.1	c.217-10785G>T		intron_variant	Intron 2 of 3		XP_047295524.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;