rs1314589

Variant names:

• chr10-128331802-A-T
• rs1314589

Variant summary

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

The variant allele was found at a frequency of 0.191 in 152,060 control chromosomes in the GnomAD database, including 2,900 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 0.19 (2900 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29085 AN: 151942 Hom.: 2901 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.191 AC: 29079 AN: 152060 Hom.: 2900 Cov.: 31 AF XY: 0.193 AC XY: 14340 AN XY: 74318

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.205

Alfa AF: 0.203 Hom.: 406

Bravo AF: 0.188

Asia WGS AF: 0.125 AC: 433 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	0.15
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1314589; hg19: chr10-130130066;