rs10489710

Variant names:

• chr1-185674866-C-T
• rs10489710
• XR_001738340.2:n.1067-4583C>T

Variant summary

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

The XR_001738340.2(LOC107985239):​n.1067-4583C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 152,174 control chromosomes in the GnomAD database, including 390 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 0.045 (390 hom., cov: 32)
• Consequence: LOC107985239 XR_001738340.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

LOC107985239 (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 (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985239	XR_001738340.2	n.1067-4583C>T		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6877 AN: 152056 Hom.: 382 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.00208

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00715

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0454 AC: 6908 AN: 152174 Hom.: 390 Cov.: 32 AF XY: 0.0439 AC XY: 3263 AN XY: 74394

Gnomad4 AFR AF: 0.130 AC: 0.130333 AN: 0.130333

Gnomad4 AMR AF: 0.0239 AC: 0.0238812 AN: 0.0238812

Gnomad4 ASJ AF: 0.0502 AC: 0.050173 AN: 0.050173

Gnomad4 EAS AF: 0.0351 AC: 0.0351351 AN: 0.0351351

Gnomad4 SAS AF: 0.0323 AC: 0.0322981 AN: 0.0322981

Gnomad4 FIN AF: 0.00208 AC: 0.00207586 AN: 0.00207586

Gnomad4 NFE AF: 0.00715 AC: 0.00714643 AN: 0.00714643

Gnomad4 OTH AF: 0.0487 AC: 0.0486767 AN: 0.0486767

Alfa AF: 0.0345 Hom.: 42

Bravo AF: 0.0526

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489710; hg19: chr1-185643998;