rs10489007

Variant names:

• chr4-31716823-A-C
• rs10489007
• XR_925555.1:n.193+302T>G

Variant summary

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

The XR_925555.1(LOC105374566):​n.193+302T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,738 control chromosomes in the GnomAD database, including 1,076 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 0.10 (1076 hom., cov: 32)
• Consequence: LOC105374566 XR_925555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 2 publications found

Genes affected

LOC105374566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374566	XR_925555.1	n.193+302T>G		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15658 AN: 151620 Hom.: 1076 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.103 AC: 15662 AN: 151738 Hom.: 1076 Cov.: 32 AF XY: 0.104 AC XY: 7697 AN XY: 74154

African (AFR) AF: 0.0275 AC: 1143 AN: 41506

American (AMR) AF: 0.0842 AC: 1279 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3460

East Asian (EAS) AF: 0.0507 AC: 261 AN: 5150

South Asian (SAS) AF: 0.0919 AC: 443 AN: 4820

European-Finnish (FIN) AF: 0.180 AC: 1910 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9869 AN: 67714

Other (OTH) AF: 0.109 AC: 230 AN: 2104

Alfa AF: 0.136 Hom.: 841

Bravo AF: 0.0940

Asia WGS AF: 0.0840 AC: 293 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.33
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10489007; hg19: chr4-31718445;