rs1314589

Variant names:

• chr10-128331802-A-T
• rs1314589

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.160 AC: 6646 AN: 41494

American (AMR) AF: 0.214 AC: 3271 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 786 AN: 3472

East Asian (EAS) AF: 0.120 AC: 622 AN: 5174

South Asian (SAS) AF: 0.132 AC: 637 AN: 4828

European-Finnish (FIN) AF: 0.244 AC: 2577 AN: 10558

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13794 AN: 67954

Other (OTH) AF: 0.205 AC: 434 AN: 2114

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1314589; hg19: chr10-130130066;