rs9841287

Variant names:

• chr3-67310-A-G
• rs9841287
• XR_940533.2:n.124-15A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-67310-A-G
• chr3-67310-A-T

Variant summary

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

The XR_940533.2(LOC105376921):​n.124-15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,928 control chromosomes in the GnomAD database, including 4,118 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 (4118 hom., cov: 31)
• Consequence: LOC105376921 XR_940533.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 13 publications found

Genes affected

LOC105376921 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376921	XR_940533.2	n.124-15A>G		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33501 AN: 151810 Hom.: 4115 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.221 AC: 33526 AN: 151928 Hom.: 4118 Cov.: 31 AF XY: 0.225 AC XY: 16694 AN XY: 74224

African (AFR) AF: 0.266 AC: 11024 AN: 41438

American (AMR) AF: 0.258 AC: 3939 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2329 AN: 5148

South Asian (SAS) AF: 0.272 AC: 1302 AN: 4790

European-Finnish (FIN) AF: 0.221 AC: 2335 AN: 10552

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11325 AN: 67968

Other (OTH) AF: 0.219 AC: 463 AN: 2110

Alfa AF: 0.188 Hom.: 10435

Bravo AF: 0.228

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.66
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs9841287; hg19: chr3-108993;