rs1230094

Variant names:

• chr17-45392790-G-A
• rs1230094

Your query was ambiguous. Multiple possible variants found:

• chr17-45392790-G-A
• chr17-45392790-G-C
• chr17-45392790-G-T

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 0.361 in 152,096 control chromosomes in the GnomAD database, including 10,525 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 0.36 (10525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410

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 (AFR) allele frequency at 95% confidence interval = 0.488 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: 0.361 AC: 54810 AN: 151978 Hom.: 10513 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.361 AC: 54861 AN: 152096 Hom.: 10525 Cov.: 33 AF XY: 0.362 AC XY: 26884 AN XY: 74352

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.378

Alfa AF: 0.305 Hom.: 9518

Bravo AF: 0.370

Asia WGS AF: 0.412 AC: 1432 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	5.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1230094; hg19: chr17-43470156;