rs10489338

chr1-209581016-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001738443.2(LOC107985256):n.166-3319T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

Genes affected

LOC107985256 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985256	XR_001738443.2	n.166-3319T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.00375

Gnomad4 AMR AF: 0.0353

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.0352

Gnomad4 FIN AF: 0.00640

Gnomad4 NFE AF: 0.0124

Gnomad4 OTH AF: 0.0284

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.69
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489338; hg19: chr1-209754361;