rs10489338

Variant names:

• chr1-209581016-A-G
• rs10489338
• XR_001738443.2:n.166-3319T>C

Variant summary

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

The XR_001738443.2(LOC107985256):​n.166-3319T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 152,344 control chromosomes in the GnomAD database, including 174 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 0.021 (174 hom., cov: 32)
• Consequence: LOC107985256 XR_001738443.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 2 publications found

Genes affected

LOC107985256 (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 (EAS) allele frequency at 95% confidence interval = 0.229 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: 0.0207 AC: 3145 AN: 152226 Hom.: 174 Cov.: 32

Gnomad AFR AF: 0.00376

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.00640

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0207 AC: 3146 AN: 152344 Hom.: 174 Cov.: 32 AF XY: 0.0220 AC XY: 1636 AN XY: 74502

African (AFR) AF: 0.00375 AC: 156 AN: 41582

American (AMR) AF: 0.0353 AC: 540 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1244 AN: 5182

South Asian (SAS) AF: 0.0352 AC: 170 AN: 4830

European-Finnish (FIN) AF: 0.00640 AC: 68 AN: 10628

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0124 AC: 843 AN: 68030

Other (OTH) AF: 0.0284 AC: 60 AN: 2114

Alfa AF: 0.0143 Hom.: 5

Bravo AF: 0.0260

Asia WGS AF: 0.111 AC: 386 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	0.69
DANN	Benign	0.64
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10489338; hg19: chr1-209754361;